niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_robust_template.py

@@ -0,0 +1,622 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_ROBUST_TEMPLATE_METADATA = Metadata(
+    id="e6d86749b113688755af2fc89adaf79f55c6735f.boutiques",
+    name="mri_robust_template",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriRobustTemplateParameters = typing.TypedDict('MriRobustTemplateParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_robust_template"],
+    "mov_files": list[InputPathType],
+    "template_file": str,
+    "sat_value": typing.NotRequired[float | None],
+    "satit_flag": bool,
+    "lta_files": typing.NotRequired[list[str] | None],
+    "mapmov_files": typing.NotRequired[list[str] | None],
+    "mapmovhdr_files": typing.NotRequired[list[str] | None],
+    "weights_files": typing.NotRequired[list[str] | None],
+    "oneminusw_flag": bool,
+    "average_type": typing.NotRequired[int | None],
+    "inittp": typing.NotRequired[int | None],
+    "fixtp_flag": bool,
+    "iscale_flag": bool,
+    "iscaleonly_flag": bool,
+    "iscalein_files": typing.NotRequired[list[str] | None],
+    "iscaleout_files": typing.NotRequired[list[str] | None],
+    "transonly_flag": bool,
+    "affine_flag": bool,
+    "ixforms_files": typing.NotRequired[list[str] | None],
+    "masks_files": typing.NotRequired[list[str] | None],
+    "vox2vox_flag": bool,
+    "leastsquares_flag": bool,
+    "noit_flag": bool,
+    "maxit": typing.NotRequired[int | None],
+    "highit": typing.NotRequired[int | None],
+    "epsit": typing.NotRequired[float | None],
+    "pairmaxit": typing.NotRequired[int | None],
+    "pairepsit": typing.NotRequired[float | None],
+    "subsample": typing.NotRequired[int | None],
+    "nomulti_flag": bool,
+    "floattype_flag": bool,
+    "finalnearest_flag": bool,
+    "doubleprec_flag": bool,
+    "cras_flag": bool,
+    "res_thresh": typing.NotRequired[float | None],
+    "frobnorm_thresh": typing.NotRequired[float | None],
+    "debug_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 {
+        "mri_robust_template": mri_robust_template_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_robust_template": mri_robust_template_outputs,
+    }.get(t)
+
+
+class MriRobustTemplateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_robust_template(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_template: OutputPathType
+    """Output template volume (final mean/median image)."""
+    output_lta_transform: OutputPathType
+    """Output transform file."""
+    output_mapped_image: OutputPathType
+    """Output mapped and resampled image."""
+    output_weights_map: OutputPathType
+    """Output weights map (outliers)."""
+
+
+def mri_robust_template_params(
+    mov_files: list[InputPathType],
+    template_file: str,
+    sat_value: float | None = None,
+    satit_flag: bool = False,
+    lta_files: list[str] | None = None,
+    mapmov_files: list[str] | None = None,
+    mapmovhdr_files: list[str] | None = None,
+    weights_files: list[str] | None = None,
+    oneminusw_flag: bool = False,
+    average_type: int | None = None,
+    inittp: int | None = None,
+    fixtp_flag: bool = False,
+    iscale_flag: bool = False,
+    iscaleonly_flag: bool = False,
+    iscalein_files: list[str] | None = None,
+    iscaleout_files: list[str] | None = None,
+    transonly_flag: bool = False,
+    affine_flag: bool = False,
+    ixforms_files: list[str] | None = None,
+    masks_files: list[str] | None = None,
+    vox2vox_flag: bool = False,
+    leastsquares_flag: bool = False,
+    noit_flag: bool = False,
+    maxit: int | None = None,
+    highit: int | None = None,
+    epsit: float | None = None,
+    pairmaxit: int | None = None,
+    pairepsit: float | None = None,
+    subsample: int | None = None,
+    nomulti_flag: bool = False,
+    floattype_flag: bool = False,
+    finalnearest_flag: bool = False,
+    doubleprec_flag: bool = False,
+    cras_flag: bool = False,
+    res_thresh: float | None = None,
+    frobnorm_thresh: float | None = None,
+    debug_flag: bool = False,
+) -> MriRobustTemplateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        mov_files: Input movable volumes to be aligned to common mean/median\
+            template.
+        template_file: Output template volume (final mean/median image).
+        sat_value: Set outlier sensitivity manually. Higher values mean less\
+            sensitivity.
+        satit_flag: Auto-detect good sensitivity (recommended for head or full\
+            brain scans).
+        lta_files: Output transforms to template (for each input).
+        mapmov_files: Output images: map and resample each input to template.
+        mapmovhdr_files: Output images: header-adjusted movables (no\
+            resampling).
+        weights_files: Output weights (outliers) in target space.
+        oneminusw_flag: Weights (outlier) map will be inverted (0=outlier), as\
+            in earlier versions.
+        average_type: Construct template from: 0 Mean, 1 Median (default).
+        inittp: Use TP# for spatial init (default random), 0: no init.
+        fixtp_flag: Map everything to init TP# (init TP is not resampled).
+        iscale_flag: Allow also intensity scaling (default off).
+        iscaleonly_flag: Only perform iscale (no transformation, default off).
+        iscalein_files: Use initial intensity scales.
+        iscaleout_files: Output final intensity scales (will activate\
+            --iscale).
+        transonly_flag: Find 3 parameter translation only.
+        affine_flag: Find 12 parameter affine transform.
+        ixforms_files: Use initial transforms (lta) on source ('id'=identity).
+        masks_files: Input masks applied to movables.
+        vox2vox_flag: Output VOX2VOX lta file (default is RAS2RAS).
+        leastsquares_flag: Use least squares instead of robust M-estimator (for\
+            testing only).
+        noit_flag: Do not iterate, just create first template.
+        maxit: Iterate max # times (if #tp>2 default 6, else 5 for 2tp reg.).
+        highit: Iterate max # times on highest resolution (default 5).
+        epsit: Stop iterations when all transform updates fall below the\
+            specified value.
+        pairmaxit: Iterate max # times (default 5) for individual pairwise\
+            registrations.
+        pairepsit: Stop individual pairwise registration iterations when\
+            transform updates fall below the specified value.
+        subsample: Subsample if dimension > specified value on all axes\
+            (default no subsampling).
+        nomulti_flag: Do not use multi-resolution (only highest resolution).
+        floattype_flag: Convert images to float internally (default: keep input\
+            type).
+        finalnearest_flag: Use nearest neighbor in final interpolation when\
+            creating average.
+        doubleprec_flag: Use double precision instead of float internally\
+            (large memory usage).
+        cras_flag: Center template at average CRAS, instead of average\
+            barycenter.
+        res_thresh: Volume resolution threshold (default is 0.01 mm).
+        frobnorm_thresh: Matrix frobenius norm threshold (default is 0.0001).
+        debug_flag: Show debug output (default no debug output).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_robust_template",
+        "mov_files": mov_files,
+        "template_file": template_file,
+        "satit_flag": satit_flag,
+        "oneminusw_flag": oneminusw_flag,
+        "fixtp_flag": fixtp_flag,
+        "iscale_flag": iscale_flag,
+        "iscaleonly_flag": iscaleonly_flag,
+        "transonly_flag": transonly_flag,
+        "affine_flag": affine_flag,
+        "vox2vox_flag": vox2vox_flag,
+        "leastsquares_flag": leastsquares_flag,
+        "noit_flag": noit_flag,
+        "nomulti_flag": nomulti_flag,
+        "floattype_flag": floattype_flag,
+        "finalnearest_flag": finalnearest_flag,
+        "doubleprec_flag": doubleprec_flag,
+        "cras_flag": cras_flag,
+        "debug_flag": debug_flag,
+    }
+    if sat_value is not None:
+        params["sat_value"] = sat_value
+    if lta_files is not None:
+        params["lta_files"] = lta_files
+    if mapmov_files is not None:
+        params["mapmov_files"] = mapmov_files
+    if mapmovhdr_files is not None:
+        params["mapmovhdr_files"] = mapmovhdr_files
+    if weights_files is not None:
+        params["weights_files"] = weights_files
+    if average_type is not None:
+        params["average_type"] = average_type
+    if inittp is not None:
+        params["inittp"] = inittp
+    if iscalein_files is not None:
+        params["iscalein_files"] = iscalein_files
+    if iscaleout_files is not None:
+        params["iscaleout_files"] = iscaleout_files
+    if ixforms_files is not None:
+        params["ixforms_files"] = ixforms_files
+    if masks_files is not None:
+        params["masks_files"] = masks_files
+    if maxit is not None:
+        params["maxit"] = maxit
+    if highit is not None:
+        params["highit"] = highit
+    if epsit is not None:
+        params["epsit"] = epsit
+    if pairmaxit is not None:
+        params["pairmaxit"] = pairmaxit
+    if pairepsit is not None:
+        params["pairepsit"] = pairepsit
+    if subsample is not None:
+        params["subsample"] = subsample
+    if res_thresh is not None:
+        params["res_thresh"] = res_thresh
+    if frobnorm_thresh is not None:
+        params["frobnorm_thresh"] = frobnorm_thresh
+    return params
+
+
+def mri_robust_template_cargs(
+    params: MriRobustTemplateParameters,
+    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_robust_template")
+    cargs.extend([
+        "-mov",
+        *[execution.input_file(f) for f in params.get("mov_files")]
+    ])
+    cargs.extend([
+        "-template",
+        params.get("template_file")
+    ])
+    if params.get("sat_value") is not None:
+        cargs.extend([
+            "--sat",
+            str(params.get("sat_value"))
+        ])
+    if params.get("satit_flag"):
+        cargs.append("--satit")
+    if params.get("lta_files") is not None:
+        cargs.extend([
+            "--lta",
+            *params.get("lta_files")
+        ])
+    if params.get("mapmov_files") is not None:
+        cargs.extend([
+            "--mapmov",
+            *params.get("mapmov_files")
+        ])
+    if params.get("mapmovhdr_files") is not None:
+        cargs.extend([
+            "--mapmovhdr",
+            *params.get("mapmovhdr_files")
+        ])
+    if params.get("weights_files") is not None:
+        cargs.extend([
+            "--weights",
+            *params.get("weights_files")
+        ])
+    if params.get("oneminusw_flag"):
+        cargs.append("--oneminusw")
+    if params.get("average_type") is not None:
+        cargs.extend([
+            "--average",
+            str(params.get("average_type"))
+        ])
+    if params.get("inittp") is not None:
+        cargs.extend([
+            "--inittp",
+            str(params.get("inittp"))
+        ])
+    if params.get("fixtp_flag"):
+        cargs.append("--fixtp")
+    if params.get("iscale_flag"):
+        cargs.append("--iscale")
+    if params.get("iscaleonly_flag"):
+        cargs.append("--iscaleonly")
+    if params.get("iscalein_files") is not None:
+        cargs.extend([
+            "--iscalein",
+            *params.get("iscalein_files")
+        ])
+    if params.get("iscaleout_files") is not None:
+        cargs.extend([
+            "--iscaleout",
+            *params.get("iscaleout_files")
+        ])
+    if params.get("transonly_flag"):
+        cargs.append("--transonly")
+    if params.get("affine_flag"):
+        cargs.append("--affine")
+    if params.get("ixforms_files") is not None:
+        cargs.extend([
+            "--ixforms",
+            *params.get("ixforms_files")
+        ])
+    if params.get("masks_files") is not None:
+        cargs.extend([
+            "--masks",
+            *params.get("masks_files")
+        ])
+    if params.get("vox2vox_flag"):
+        cargs.append("--vox2vox")
+    if params.get("leastsquares_flag"):
+        cargs.append("--leastsquares")
+    if params.get("noit_flag"):
+        cargs.append("--noit")
+    if params.get("maxit") is not None:
+        cargs.extend([
+            "--maxit",
+            str(params.get("maxit"))
+        ])
+    if params.get("highit") is not None:
+        cargs.extend([
+            "--highit",
+            str(params.get("highit"))
+        ])
+    if params.get("epsit") is not None:
+        cargs.extend([
+            "--epsit",
+            str(params.get("epsit"))
+        ])
+    if params.get("pairmaxit") is not None:
+        cargs.extend([
+            "--pairmaxit",
+            str(params.get("pairmaxit"))
+        ])
+    if params.get("pairepsit") is not None:
+        cargs.extend([
+            "--pairepsit",
+            str(params.get("pairepsit"))
+        ])
+    if params.get("subsample") is not None:
+        cargs.extend([
+            "--subsample",
+            str(params.get("subsample"))
+        ])
+    if params.get("nomulti_flag"):
+        cargs.append("--nomulti")
+    if params.get("floattype_flag"):
+        cargs.append("--floattype")
+    if params.get("finalnearest_flag"):
+        cargs.append("--finalnearest")
+    if params.get("doubleprec_flag"):
+        cargs.append("--doubleprec")
+    if params.get("cras_flag"):
+        cargs.append("--cras")
+    if params.get("res_thresh") is not None:
+        cargs.extend([
+            "--res-thresh",
+            str(params.get("res_thresh"))
+        ])
+    if params.get("frobnorm_thresh") is not None:
+        cargs.extend([
+            "--frobnorm-thresh",
+            str(params.get("frobnorm_thresh"))
+        ])
+    if params.get("debug_flag"):
+        cargs.append("--debug")
+    return cargs
+
+
+def mri_robust_template_outputs(
+    params: MriRobustTemplateParameters,
+    execution: Execution,
+) -> MriRobustTemplateOutputs:
+    """
+    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 = MriRobustTemplateOutputs(
+        root=execution.output_file("."),
+        output_template=execution.output_file(params.get("template_file")),
+        output_lta_transform=execution.output_file("[TMP_NAME].lta"),
+        output_mapped_image=execution.output_file("[TMP_NAME]_to_template.mgz"),
+        output_weights_map=execution.output_file("[TMP_NAME]_weights.mgz"),
+    )
+    return ret
+
+
+def mri_robust_template_execute(
+    params: MriRobustTemplateParameters,
+    execution: Execution,
+) -> MriRobustTemplateOutputs:
+    """
+    Constructs an unbiased robust template for longitudinal volumes using an
+    iterative method.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriRobustTemplateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_robust_template_cargs(params, execution)
+    ret = mri_robust_template_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_robust_template(
+    mov_files: list[InputPathType],
+    template_file: str,
+    sat_value: float | None = None,
+    satit_flag: bool = False,
+    lta_files: list[str] | None = None,
+    mapmov_files: list[str] | None = None,
+    mapmovhdr_files: list[str] | None = None,
+    weights_files: list[str] | None = None,
+    oneminusw_flag: bool = False,
+    average_type: int | None = None,
+    inittp: int | None = None,
+    fixtp_flag: bool = False,
+    iscale_flag: bool = False,
+    iscaleonly_flag: bool = False,
+    iscalein_files: list[str] | None = None,
+    iscaleout_files: list[str] | None = None,
+    transonly_flag: bool = False,
+    affine_flag: bool = False,
+    ixforms_files: list[str] | None = None,
+    masks_files: list[str] | None = None,
+    vox2vox_flag: bool = False,
+    leastsquares_flag: bool = False,
+    noit_flag: bool = False,
+    maxit: int | None = None,
+    highit: int | None = None,
+    epsit: float | None = None,
+    pairmaxit: int | None = None,
+    pairepsit: float | None = None,
+    subsample: int | None = None,
+    nomulti_flag: bool = False,
+    floattype_flag: bool = False,
+    finalnearest_flag: bool = False,
+    doubleprec_flag: bool = False,
+    cras_flag: bool = False,
+    res_thresh: float | None = None,
+    frobnorm_thresh: float | None = None,
+    debug_flag: bool = False,
+    runner: Runner | None = None,
+) -> MriRobustTemplateOutputs:
+    """
+    Constructs an unbiased robust template for longitudinal volumes using an
+    iterative method.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        mov_files: Input movable volumes to be aligned to common mean/median\
+            template.
+        template_file: Output template volume (final mean/median image).
+        sat_value: Set outlier sensitivity manually. Higher values mean less\
+            sensitivity.
+        satit_flag: Auto-detect good sensitivity (recommended for head or full\
+            brain scans).
+        lta_files: Output transforms to template (for each input).
+        mapmov_files: Output images: map and resample each input to template.
+        mapmovhdr_files: Output images: header-adjusted movables (no\
+            resampling).
+        weights_files: Output weights (outliers) in target space.
+        oneminusw_flag: Weights (outlier) map will be inverted (0=outlier), as\
+            in earlier versions.
+        average_type: Construct template from: 0 Mean, 1 Median (default).
+        inittp: Use TP# for spatial init (default random), 0: no init.
+        fixtp_flag: Map everything to init TP# (init TP is not resampled).
+        iscale_flag: Allow also intensity scaling (default off).
+        iscaleonly_flag: Only perform iscale (no transformation, default off).
+        iscalein_files: Use initial intensity scales.
+        iscaleout_files: Output final intensity scales (will activate\
+            --iscale).
+        transonly_flag: Find 3 parameter translation only.
+        affine_flag: Find 12 parameter affine transform.
+        ixforms_files: Use initial transforms (lta) on source ('id'=identity).
+        masks_files: Input masks applied to movables.
+        vox2vox_flag: Output VOX2VOX lta file (default is RAS2RAS).
+        leastsquares_flag: Use least squares instead of robust M-estimator (for\
+            testing only).
+        noit_flag: Do not iterate, just create first template.
+        maxit: Iterate max # times (if #tp>2 default 6, else 5 for 2tp reg.).
+        highit: Iterate max # times on highest resolution (default 5).
+        epsit: Stop iterations when all transform updates fall below the\
+            specified value.
+        pairmaxit: Iterate max # times (default 5) for individual pairwise\
+            registrations.
+        pairepsit: Stop individual pairwise registration iterations when\
+            transform updates fall below the specified value.
+        subsample: Subsample if dimension > specified value on all axes\
+            (default no subsampling).
+        nomulti_flag: Do not use multi-resolution (only highest resolution).
+        floattype_flag: Convert images to float internally (default: keep input\
+            type).
+        finalnearest_flag: Use nearest neighbor in final interpolation when\
+            creating average.
+        doubleprec_flag: Use double precision instead of float internally\
+            (large memory usage).
+        cras_flag: Center template at average CRAS, instead of average\
+            barycenter.
+        res_thresh: Volume resolution threshold (default is 0.01 mm).
+        frobnorm_thresh: Matrix frobenius norm threshold (default is 0.0001).
+        debug_flag: Show debug output (default no debug output).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriRobustTemplateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_ROBUST_TEMPLATE_METADATA)
+    params = mri_robust_template_params(
+        mov_files=mov_files,
+        template_file=template_file,
+        sat_value=sat_value,
+        satit_flag=satit_flag,
+        lta_files=lta_files,
+        mapmov_files=mapmov_files,
+        mapmovhdr_files=mapmovhdr_files,
+        weights_files=weights_files,
+        oneminusw_flag=oneminusw_flag,
+        average_type=average_type,
+        inittp=inittp,
+        fixtp_flag=fixtp_flag,
+        iscale_flag=iscale_flag,
+        iscaleonly_flag=iscaleonly_flag,
+        iscalein_files=iscalein_files,
+        iscaleout_files=iscaleout_files,
+        transonly_flag=transonly_flag,
+        affine_flag=affine_flag,
+        ixforms_files=ixforms_files,
+        masks_files=masks_files,
+        vox2vox_flag=vox2vox_flag,
+        leastsquares_flag=leastsquares_flag,
+        noit_flag=noit_flag,
+        maxit=maxit,
+        highit=highit,
+        epsit=epsit,
+        pairmaxit=pairmaxit,
+        pairepsit=pairepsit,
+        subsample=subsample,
+        nomulti_flag=nomulti_flag,
+        floattype_flag=floattype_flag,
+        finalnearest_flag=finalnearest_flag,
+        doubleprec_flag=doubleprec_flag,
+        cras_flag=cras_flag,
+        res_thresh=res_thresh,
+        frobnorm_thresh=frobnorm_thresh,
+        debug_flag=debug_flag,
+    )
+    return mri_robust_template_execute(params, execution)
+
+
+__all__ = [
+    "MRI_ROBUST_TEMPLATE_METADATA",
+    "MriRobustTemplateOutputs",
+    "MriRobustTemplateParameters",
+    "mri_robust_template",
+    "mri_robust_template_params",
+]