niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_rf_label.py

@@ -0,0 +1,641 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_RF_LABEL_METADATA = Metadata(
+    id="4696827fae4b209c83ac56d628b74442e0fa9ece.boutiques",
+    name="mri_rf_label",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriRfLabelParameters = typing.TypedDict('MriRfLabelParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_rf_label"],
+    "input_volumes": list[InputPathType],
+    "transform_file": InputPathType,
+    "gcafile": InputPathType,
+    "output_volume": str,
+    "cross_sequence_flag": bool,
+    "nogibbs_flag": bool,
+    "wm_path": typing.NotRequired[InputPathType | None],
+    "conform_flag": bool,
+    "normpd_flag": bool,
+    "gca_tl": typing.NotRequired[InputPathType | None],
+    "debug_voxel": typing.NotRequired[list[float] | None],
+    "debug_node": typing.NotRequired[list[float] | None],
+    "debug_label": typing.NotRequired[float | None],
+    "tr": typing.NotRequired[float | None],
+    "te": typing.NotRequired[float | None],
+    "alpha": typing.NotRequired[float | None],
+    "example": typing.NotRequired[list[InputPathType] | None],
+    "pthresh": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[float | None],
+    "novar_flag": bool,
+    "regularize": typing.NotRequired[float | None],
+    "nohippo_flag": bool,
+    "fwm": typing.NotRequired[InputPathType | None],
+    "mri_vol": typing.NotRequired[InputPathType | None],
+    "heq": typing.NotRequired[InputPathType | None],
+    "renorm": typing.NotRequired[InputPathType | None],
+    "flash_flag": bool,
+    "flash_params": typing.NotRequired[InputPathType | None],
+    "renormalize": typing.NotRequired[list[float] | None],
+    "set_input": typing.NotRequired[InputPathType | None],
+    "histogram_flag": bool,
+    "cond_density_mean": typing.NotRequired[float | None],
+    "snapshots": typing.NotRequired[list[str] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "expand": typing.NotRequired[float | None],
+    "max_iter": typing.NotRequired[float | None],
+    "filter_mode": typing.NotRequired[list[float] | None],
+    "longitudinal_vol": typing.NotRequired[InputPathType | None],
+    "longitudinal_lta": typing.NotRequired[InputPathType | None],
+    "relabel_unlikely_flag": typing.NotRequired[list[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_rf_label": mri_rf_label_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_rf_label": mri_rf_label_outputs,
+    }.get(t)
+
+
+class MriRfLabelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_rf_label(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outvol: OutputPathType
+    """Output volume from mri_ca_label"""
+
+
+def mri_rf_label_params(
+    input_volumes: list[InputPathType],
+    transform_file: InputPathType,
+    gcafile: InputPathType,
+    output_volume: str,
+    cross_sequence_flag: bool = False,
+    nogibbs_flag: bool = False,
+    wm_path: InputPathType | None = None,
+    conform_flag: bool = False,
+    normpd_flag: bool = False,
+    gca_tl: InputPathType | None = None,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    debug_label: float | None = None,
+    tr: float | None = None,
+    te: float | None = None,
+    alpha: float | None = None,
+    example: list[InputPathType] | None = None,
+    pthresh: float | None = 0.7,
+    niter: float | None = 2,
+    novar_flag: bool = False,
+    regularize: float | None = None,
+    nohippo_flag: bool = False,
+    fwm: InputPathType | None = None,
+    mri_vol: InputPathType | None = None,
+    heq: InputPathType | None = None,
+    renorm: InputPathType | None = None,
+    flash_flag: bool = False,
+    flash_params: InputPathType | None = None,
+    renormalize: list[float] | None = None,
+    set_input: InputPathType | None = None,
+    histogram_flag: bool = False,
+    cond_density_mean: float | None = None,
+    snapshots: list[str] | None = None,
+    mask: InputPathType | None = None,
+    expand: float | None = None,
+    max_iter: float | None = 200,
+    filter_mode: list[float] | None = [0, 0.5],
+    longitudinal_vol: InputPathType | None = None,
+    longitudinal_lta: InputPathType | None = None,
+    relabel_unlikely_flag: list[float] | None = None,
+) -> MriRfLabelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volumes: Input volume(s).
+        transform_file: Transform file.
+        gcafile: GCA file.
+        output_volume: Output volume.
+        cross_sequence_flag: Label a volume acquired with a sequence different\
+            than atlas.
+        nogibbs_flag: Disable gibbs priors.
+        wm_path: Use WM segmentation from provided file.
+        conform_flag: Interpolate volume to be isotropic 1mm^3.
+        normpd_flag: Normalize PD image to GCA means.
+        gca_tl: Use file to label the thin temporal lobe.
+        debug_voxel: Debug voxel at specified coordinates.
+        debug_node: Debug node at specified coordinates.
+        debug_label: Debug label at specified index.
+        tr: Set TR in msec.
+        te: Set TE in msec.
+        alpha: Set alpha in radians.
+        example: Use T1 (mri_vol) and segmentation as example.
+        pthresh: Use p threshold for adaptive renormalization.
+        niter: Apply max likelihood for n iterations.
+        novar_flag: Do not use variance in classification.
+        regularize: Regularize variance to be sigma+nC(noise).
+        nohippo_flag: Do not auto-edit hippocampus.
+        fwm: Use fixed white matter segmentation from wm.
+        mri_vol: Write most likely MR volume to specified file.
+        heq: Use histogram equalization from specified volume.
+        renorm: Renormalize using predicted intensity values.
+        flash_flag: Use FLASH forward model to predict intensity values.
+        flash_params: Use FLASH forward model and tissue params from file.
+        renormalize: Renorm class means iter times after initial label with\
+            window of wsize.
+        set_input: Set input volume.
+        histogram_flag: Use GCA to histogram normalize input image.
+        cond_density_mean: Mean filter n times to conditional densities.
+        snapshots: Write snapshots of gibbs process every n times to filename.
+        mask: Use mri_vol to mask final labeling.
+        expand: Expand.
+        max_iter: Set max iterations.
+        filter_mode: Filter labeled volume with threshold t mode filter f times.
+        longitudinal_vol: Longitudinal processing: mri_vol is label from tp1,\
+            LTA is registration from tp1 to current data.
+        longitudinal_lta: Longitudinal LTA registration.
+        relabel_unlikely_flag: Reclassify voxels using a Gaussian window to\
+            recomute priors and likelihoods.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_rf_label",
+        "input_volumes": input_volumes,
+        "transform_file": transform_file,
+        "gcafile": gcafile,
+        "output_volume": output_volume,
+        "cross_sequence_flag": cross_sequence_flag,
+        "nogibbs_flag": nogibbs_flag,
+        "conform_flag": conform_flag,
+        "normpd_flag": normpd_flag,
+        "novar_flag": novar_flag,
+        "nohippo_flag": nohippo_flag,
+        "flash_flag": flash_flag,
+        "histogram_flag": histogram_flag,
+    }
+    if wm_path is not None:
+        params["wm_path"] = wm_path
+    if gca_tl is not None:
+        params["gca_tl"] = gca_tl
+    if debug_voxel is not None:
+        params["debug_voxel"] = debug_voxel
+    if debug_node is not None:
+        params["debug_node"] = debug_node
+    if debug_label is not None:
+        params["debug_label"] = debug_label
+    if tr is not None:
+        params["tr"] = tr
+    if te is not None:
+        params["te"] = te
+    if alpha is not None:
+        params["alpha"] = alpha
+    if example is not None:
+        params["example"] = example
+    if pthresh is not None:
+        params["pthresh"] = pthresh
+    if niter is not None:
+        params["niter"] = niter
+    if regularize is not None:
+        params["regularize"] = regularize
+    if fwm is not None:
+        params["fwm"] = fwm
+    if mri_vol is not None:
+        params["mri_vol"] = mri_vol
+    if heq is not None:
+        params["heq"] = heq
+    if renorm is not None:
+        params["renorm"] = renorm
+    if flash_params is not None:
+        params["flash_params"] = flash_params
+    if renormalize is not None:
+        params["renormalize"] = renormalize
+    if set_input is not None:
+        params["set_input"] = set_input
+    if cond_density_mean is not None:
+        params["cond_density_mean"] = cond_density_mean
+    if snapshots is not None:
+        params["snapshots"] = snapshots
+    if mask is not None:
+        params["mask"] = mask
+    if expand is not None:
+        params["expand"] = expand
+    if max_iter is not None:
+        params["max_iter"] = max_iter
+    if filter_mode is not None:
+        params["filter_mode"] = filter_mode
+    if longitudinal_vol is not None:
+        params["longitudinal_vol"] = longitudinal_vol
+    if longitudinal_lta is not None:
+        params["longitudinal_lta"] = longitudinal_lta
+    if relabel_unlikely_flag is not None:
+        params["relabel_unlikely_flag"] = relabel_unlikely_flag
+    return params
+
+
+def mri_rf_label_cargs(
+    params: MriRfLabelParameters,
+    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_rf_label")
+    cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
+    cargs.append(execution.input_file(params.get("transform_file")))
+    cargs.append(execution.input_file(params.get("gcafile")))
+    cargs.append(params.get("output_volume"))
+    if params.get("cross_sequence_flag"):
+        cargs.append("-cross-sequence")
+    if params.get("nogibbs_flag"):
+        cargs.append("-nogibbs")
+    if params.get("wm_path") is not None:
+        cargs.extend([
+            "-wm",
+            execution.input_file(params.get("wm_path"))
+        ])
+    if params.get("conform_flag"):
+        cargs.append("-conform")
+    if params.get("normpd_flag"):
+        cargs.append("-normpd")
+    if params.get("gca_tl") is not None:
+        cargs.extend([
+            "-tl",
+            execution.input_file(params.get("gca_tl"))
+        ])
+    if params.get("debug_voxel") is not None:
+        cargs.extend([
+            "-debug_voxel",
+            *map(str, params.get("debug_voxel"))
+        ])
+    if params.get("debug_node") is not None:
+        cargs.extend([
+            "-debug_node",
+            *map(str, params.get("debug_node"))
+        ])
+    if params.get("debug_label") is not None:
+        cargs.extend([
+            "-debug_label",
+            str(params.get("debug_label"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-tr",
+            str(params.get("tr"))
+        ])
+    if params.get("te") is not None:
+        cargs.extend([
+            "-te",
+            str(params.get("te"))
+        ])
+    if params.get("alpha") is not None:
+        cargs.extend([
+            "-alpha",
+            str(params.get("alpha"))
+        ])
+    if params.get("example") is not None:
+        cargs.extend([
+            "-example",
+            *[execution.input_file(f) for f in params.get("example")]
+        ])
+    if params.get("pthresh") is not None:
+        cargs.extend([
+            "-pthresh",
+            str(params.get("pthresh"))
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter"))
+        ])
+    if params.get("novar_flag"):
+        cargs.append("-novar")
+    if params.get("regularize") is not None:
+        cargs.extend([
+            "-regularize",
+            str(params.get("regularize"))
+        ])
+    if params.get("nohippo_flag"):
+        cargs.append("-nohippo")
+    if params.get("fwm") is not None:
+        cargs.extend([
+            "-fwm",
+            execution.input_file(params.get("fwm"))
+        ])
+    if params.get("mri_vol") is not None:
+        cargs.extend([
+            "-mri",
+            execution.input_file(params.get("mri_vol"))
+        ])
+    if params.get("heq") is not None:
+        cargs.extend([
+            "-heq",
+            execution.input_file(params.get("heq"))
+        ])
+    if params.get("renorm") is not None:
+        cargs.extend([
+            "-renorm",
+            execution.input_file(params.get("renorm"))
+        ])
+    if params.get("flash_flag"):
+        cargs.append("-flash")
+    if params.get("flash_params") is not None:
+        cargs.extend([
+            "-flash_params",
+            execution.input_file(params.get("flash_params"))
+        ])
+    if params.get("renormalize") is not None:
+        cargs.extend([
+            "-renormalize",
+            *map(str, params.get("renormalize"))
+        ])
+    if params.get("set_input") is not None:
+        cargs.extend([
+            "-r",
+            execution.input_file(params.get("set_input"))
+        ])
+    if params.get("histogram_flag"):
+        cargs.append("-h")
+    if params.get("cond_density_mean") is not None:
+        cargs.extend([
+            "-a",
+            str(params.get("cond_density_mean"))
+        ])
+    if params.get("snapshots") is not None:
+        cargs.extend([
+            "-w",
+            *params.get("snapshots")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-m",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("expand") is not None:
+        cargs.extend([
+            "-e",
+            str(params.get("expand"))
+        ])
+    if params.get("max_iter") is not None:
+        cargs.extend([
+            "-n",
+            str(params.get("max_iter"))
+        ])
+    if params.get("filter_mode") is not None:
+        cargs.extend([
+            "-f",
+            *map(str, params.get("filter_mode"))
+        ])
+    if params.get("longitudinal_vol") is not None:
+        cargs.extend([
+            "-L",
+            execution.input_file(params.get("longitudinal_vol"))
+        ])
+    if params.get("longitudinal_lta") is not None:
+        cargs.append(execution.input_file(params.get("longitudinal_lta")))
+    if params.get("relabel_unlikely_flag") is not None:
+        cargs.extend([
+            "-RELABEL_UNLIKELY",
+            *map(str, params.get("relabel_unlikely_flag"))
+        ])
+    return cargs
+
+
+def mri_rf_label_outputs(
+    params: MriRfLabelParameters,
+    execution: Execution,
+) -> MriRfLabelOutputs:
+    """
+    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 = MriRfLabelOutputs(
+        root=execution.output_file("."),
+        outvol=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mri_rf_label_execute(
+    params: MriRfLabelParameters,
+    execution: Execution,
+) -> MriRfLabelOutputs:
+    """
+    MRI automatic tissue labeling using a Gaussian Classifier Atlas (GCA).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriRfLabelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_rf_label_cargs(params, execution)
+    ret = mri_rf_label_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_rf_label(
+    input_volumes: list[InputPathType],
+    transform_file: InputPathType,
+    gcafile: InputPathType,
+    output_volume: str,
+    cross_sequence_flag: bool = False,
+    nogibbs_flag: bool = False,
+    wm_path: InputPathType | None = None,
+    conform_flag: bool = False,
+    normpd_flag: bool = False,
+    gca_tl: InputPathType | None = None,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    debug_label: float | None = None,
+    tr: float | None = None,
+    te: float | None = None,
+    alpha: float | None = None,
+    example: list[InputPathType] | None = None,
+    pthresh: float | None = 0.7,
+    niter: float | None = 2,
+    novar_flag: bool = False,
+    regularize: float | None = None,
+    nohippo_flag: bool = False,
+    fwm: InputPathType | None = None,
+    mri_vol: InputPathType | None = None,
+    heq: InputPathType | None = None,
+    renorm: InputPathType | None = None,
+    flash_flag: bool = False,
+    flash_params: InputPathType | None = None,
+    renormalize: list[float] | None = None,
+    set_input: InputPathType | None = None,
+    histogram_flag: bool = False,
+    cond_density_mean: float | None = None,
+    snapshots: list[str] | None = None,
+    mask: InputPathType | None = None,
+    expand: float | None = None,
+    max_iter: float | None = 200,
+    filter_mode: list[float] | None = [0, 0.5],
+    longitudinal_vol: InputPathType | None = None,
+    longitudinal_lta: InputPathType | None = None,
+    relabel_unlikely_flag: list[float] | None = None,
+    runner: Runner | None = None,
+) -> MriRfLabelOutputs:
+    """
+    MRI automatic tissue labeling using a Gaussian Classifier Atlas (GCA).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volumes: Input volume(s).
+        transform_file: Transform file.
+        gcafile: GCA file.
+        output_volume: Output volume.
+        cross_sequence_flag: Label a volume acquired with a sequence different\
+            than atlas.
+        nogibbs_flag: Disable gibbs priors.
+        wm_path: Use WM segmentation from provided file.
+        conform_flag: Interpolate volume to be isotropic 1mm^3.
+        normpd_flag: Normalize PD image to GCA means.
+        gca_tl: Use file to label the thin temporal lobe.
+        debug_voxel: Debug voxel at specified coordinates.
+        debug_node: Debug node at specified coordinates.
+        debug_label: Debug label at specified index.
+        tr: Set TR in msec.
+        te: Set TE in msec.
+        alpha: Set alpha in radians.
+        example: Use T1 (mri_vol) and segmentation as example.
+        pthresh: Use p threshold for adaptive renormalization.
+        niter: Apply max likelihood for n iterations.
+        novar_flag: Do not use variance in classification.
+        regularize: Regularize variance to be sigma+nC(noise).
+        nohippo_flag: Do not auto-edit hippocampus.
+        fwm: Use fixed white matter segmentation from wm.
+        mri_vol: Write most likely MR volume to specified file.
+        heq: Use histogram equalization from specified volume.
+        renorm: Renormalize using predicted intensity values.
+        flash_flag: Use FLASH forward model to predict intensity values.
+        flash_params: Use FLASH forward model and tissue params from file.
+        renormalize: Renorm class means iter times after initial label with\
+            window of wsize.
+        set_input: Set input volume.
+        histogram_flag: Use GCA to histogram normalize input image.
+        cond_density_mean: Mean filter n times to conditional densities.
+        snapshots: Write snapshots of gibbs process every n times to filename.
+        mask: Use mri_vol to mask final labeling.
+        expand: Expand.
+        max_iter: Set max iterations.
+        filter_mode: Filter labeled volume with threshold t mode filter f times.
+        longitudinal_vol: Longitudinal processing: mri_vol is label from tp1,\
+            LTA is registration from tp1 to current data.
+        longitudinal_lta: Longitudinal LTA registration.
+        relabel_unlikely_flag: Reclassify voxels using a Gaussian window to\
+            recomute priors and likelihoods.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriRfLabelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RF_LABEL_METADATA)
+    params = mri_rf_label_params(
+        input_volumes=input_volumes,
+        transform_file=transform_file,
+        gcafile=gcafile,
+        output_volume=output_volume,
+        cross_sequence_flag=cross_sequence_flag,
+        nogibbs_flag=nogibbs_flag,
+        wm_path=wm_path,
+        conform_flag=conform_flag,
+        normpd_flag=normpd_flag,
+        gca_tl=gca_tl,
+        debug_voxel=debug_voxel,
+        debug_node=debug_node,
+        debug_label=debug_label,
+        tr=tr,
+        te=te,
+        alpha=alpha,
+        example=example,
+        pthresh=pthresh,
+        niter=niter,
+        novar_flag=novar_flag,
+        regularize=regularize,
+        nohippo_flag=nohippo_flag,
+        fwm=fwm,
+        mri_vol=mri_vol,
+        heq=heq,
+        renorm=renorm,
+        flash_flag=flash_flag,
+        flash_params=flash_params,
+        renormalize=renormalize,
+        set_input=set_input,
+        histogram_flag=histogram_flag,
+        cond_density_mean=cond_density_mean,
+        snapshots=snapshots,
+        mask=mask,
+        expand=expand,
+        max_iter=max_iter,
+        filter_mode=filter_mode,
+        longitudinal_vol=longitudinal_vol,
+        longitudinal_lta=longitudinal_lta,
+        relabel_unlikely_flag=relabel_unlikely_flag,
+    )
+    return mri_rf_label_execute(params, execution)
+
+
+__all__ = [
+    "MRI_RF_LABEL_METADATA",
+    "MriRfLabelOutputs",
+    "MriRfLabelParameters",
+    "mri_rf_label",
+    "mri_rf_label_params",
+]