niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_gtmseg.py

@@ -0,0 +1,401 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_GTMSEG_METADATA = Metadata(
+    id="2c164b92c884894655aa369148327d84b308bec1.boutiques",
+    name="mri_gtmseg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriGtmsegParameters = typing.TypedDict('MriGtmsegParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_gtmseg"],
+    "output_volume": str,
+    "source_subject": str,
+    "internal_usf": typing.NotRequired[float | None],
+    "apas_file": typing.NotRequired[InputPathType | None],
+    "context_annotation": typing.NotRequired[list[str] | None],
+    "subseg_wm": bool,
+    "wm_annotation": typing.NotRequired[list[str] | None],
+    "dmax": typing.NotRequired[float | None],
+    "keep_hypo": bool,
+    "keep_cc": bool,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "lhminmax": typing.NotRequired[list[float] | None],
+    "rhminmax": typing.NotRequired[list[float] | None],
+    "output_usf": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "threads_max": bool,
+    "threads_max_1": bool,
+    "debug": bool,
+    "check_opts": 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_gtmseg": mri_gtmseg_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 MriGtmsegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_gtmseg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_gtmseg_params(
+    output_volume: str,
+    source_subject: str,
+    internal_usf: float | None = None,
+    apas_file: InputPathType | None = None,
+    context_annotation: list[str] | None = None,
+    subseg_wm: bool = False,
+    wm_annotation: list[str] | None = None,
+    dmax: float | None = None,
+    keep_hypo: bool = False,
+    keep_cc: bool = False,
+    ctab: InputPathType | None = None,
+    lhminmax: list[float] | None = None,
+    rhminmax: list[float] | None = None,
+    output_usf: float | None = None,
+    threads: float | None = None,
+    threads_max: bool = False,
+    threads_max_1: bool = False,
+    debug: bool = False,
+    check_opts: bool = False,
+) -> MriGtmsegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_volume: Output volume (output will be subject/mri/outvol).
+        source_subject: Source subject.
+        internal_usf: Upsampling factor (default 2).
+        apas_file: Defines extra-cerebral and subcortical segmentations\
+            (apas+head.mgz).
+        context_annotation: Use annotation to segment cortex\
+            (aparc.annot,1000,2000).
+        subseg_wm: Turn on segmenting of WM into smaller parts (off by default).
+        wm_annotation: Use annotation to subsegment white matter.
+        dmax: Distance from cortex for white matter segmentation to be\
+            considered 'unsegmented' (default 5.000000).
+        keep_hypo: Do not convert white matter hypointensities to a white\
+            matter label.
+        keep_cc: Do not convert corpus callosum to a white matter label.
+        ctab: Copy items in ctab.lut into master ctab merging or overwriting\
+            what is there.
+        lhminmax: For defining left hemisphere ribbon in APAS (default: 1000\
+            1900).
+        rhminmax: For defining right hemisphere ribbon in APAS (default: 2000\
+            2900).
+        output_usf: Set actual output resolution. Default is to be the same as\
+            the --internal-usf.
+        threads: Use N threads (with Open MP).
+        threads_max: Use the maximum allowable number of threads for this\
+            computer.
+        threads_max_1: Use one less than the maximum allowable number of\
+            threads for this computer.
+        debug: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_gtmseg",
+        "output_volume": output_volume,
+        "source_subject": source_subject,
+        "subseg_wm": subseg_wm,
+        "keep_hypo": keep_hypo,
+        "keep_cc": keep_cc,
+        "threads_max": threads_max,
+        "threads_max_1": threads_max_1,
+        "debug": debug,
+        "check_opts": check_opts,
+    }
+    if internal_usf is not None:
+        params["internal_usf"] = internal_usf
+    if apas_file is not None:
+        params["apas_file"] = apas_file
+    if context_annotation is not None:
+        params["context_annotation"] = context_annotation
+    if wm_annotation is not None:
+        params["wm_annotation"] = wm_annotation
+    if dmax is not None:
+        params["dmax"] = dmax
+    if ctab is not None:
+        params["ctab"] = ctab
+    if lhminmax is not None:
+        params["lhminmax"] = lhminmax
+    if rhminmax is not None:
+        params["rhminmax"] = rhminmax
+    if output_usf is not None:
+        params["output_usf"] = output_usf
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mri_gtmseg_cargs(
+    params: MriGtmsegParameters,
+    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_gtmseg")
+    cargs.extend([
+        "--o",
+        params.get("output_volume")
+    ])
+    cargs.extend([
+        "--s",
+        params.get("source_subject")
+    ])
+    if params.get("internal_usf") is not None:
+        cargs.extend([
+            "--internal-usf",
+            str(params.get("internal_usf"))
+        ])
+    if params.get("apas_file") is not None:
+        cargs.extend([
+            "--apas",
+            execution.input_file(params.get("apas_file"))
+        ])
+    if params.get("context_annotation") is not None:
+        cargs.extend([
+            "--ctx-annot",
+            *params.get("context_annotation")
+        ])
+    if params.get("subseg_wm"):
+        cargs.append("--subseg-wm")
+    if params.get("wm_annotation") is not None:
+        cargs.extend([
+            "--wm-annot",
+            *params.get("wm_annotation")
+        ])
+    if params.get("dmax") is not None:
+        cargs.extend([
+            "--dmax",
+            str(params.get("dmax"))
+        ])
+    if params.get("keep_hypo"):
+        cargs.append("--keep-hypo")
+    if params.get("keep_cc"):
+        cargs.append("--keep-cc")
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("ctab"))
+        ])
+    if params.get("lhminmax") is not None:
+        cargs.extend([
+            "--lhminmax",
+            *map(str, params.get("lhminmax"))
+        ])
+    if params.get("rhminmax") is not None:
+        cargs.extend([
+            "--rhminmax",
+            *map(str, params.get("rhminmax"))
+        ])
+    if params.get("output_usf") is not None:
+        cargs.extend([
+            "--output-usf",
+            str(params.get("output_usf"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("threads_max"):
+        cargs.append("--threads-max")
+    if params.get("threads_max_1"):
+        cargs.append("--threads-max-1")
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("check_opts"):
+        cargs.append("--checkopts")
+    return cargs
+
+
+def mri_gtmseg_outputs(
+    params: MriGtmsegParameters,
+    execution: Execution,
+) -> MriGtmsegOutputs:
+    """
+    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 = MriGtmsegOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_gtmseg_execute(
+    params: MriGtmsegParameters,
+    execution: Execution,
+) -> MriGtmsegOutputs:
+    """
+    Creates a segmentation that can be used with the geometric transfer matrix
+    (GTM).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriGtmsegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_gtmseg_cargs(params, execution)
+    ret = mri_gtmseg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_gtmseg(
+    output_volume: str,
+    source_subject: str,
+    internal_usf: float | None = None,
+    apas_file: InputPathType | None = None,
+    context_annotation: list[str] | None = None,
+    subseg_wm: bool = False,
+    wm_annotation: list[str] | None = None,
+    dmax: float | None = None,
+    keep_hypo: bool = False,
+    keep_cc: bool = False,
+    ctab: InputPathType | None = None,
+    lhminmax: list[float] | None = None,
+    rhminmax: list[float] | None = None,
+    output_usf: float | None = None,
+    threads: float | None = None,
+    threads_max: bool = False,
+    threads_max_1: bool = False,
+    debug: bool = False,
+    check_opts: bool = False,
+    runner: Runner | None = None,
+) -> MriGtmsegOutputs:
+    """
+    Creates a segmentation that can be used with the geometric transfer matrix
+    (GTM).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        output_volume: Output volume (output will be subject/mri/outvol).
+        source_subject: Source subject.
+        internal_usf: Upsampling factor (default 2).
+        apas_file: Defines extra-cerebral and subcortical segmentations\
+            (apas+head.mgz).
+        context_annotation: Use annotation to segment cortex\
+            (aparc.annot,1000,2000).
+        subseg_wm: Turn on segmenting of WM into smaller parts (off by default).
+        wm_annotation: Use annotation to subsegment white matter.
+        dmax: Distance from cortex for white matter segmentation to be\
+            considered 'unsegmented' (default 5.000000).
+        keep_hypo: Do not convert white matter hypointensities to a white\
+            matter label.
+        keep_cc: Do not convert corpus callosum to a white matter label.
+        ctab: Copy items in ctab.lut into master ctab merging or overwriting\
+            what is there.
+        lhminmax: For defining left hemisphere ribbon in APAS (default: 1000\
+            1900).
+        rhminmax: For defining right hemisphere ribbon in APAS (default: 2000\
+            2900).
+        output_usf: Set actual output resolution. Default is to be the same as\
+            the --internal-usf.
+        threads: Use N threads (with Open MP).
+        threads_max: Use the maximum allowable number of threads for this\
+            computer.
+        threads_max_1: Use one less than the maximum allowable number of\
+            threads for this computer.
+        debug: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriGtmsegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GTMSEG_METADATA)
+    params = mri_gtmseg_params(
+        output_volume=output_volume,
+        source_subject=source_subject,
+        internal_usf=internal_usf,
+        apas_file=apas_file,
+        context_annotation=context_annotation,
+        subseg_wm=subseg_wm,
+        wm_annotation=wm_annotation,
+        dmax=dmax,
+        keep_hypo=keep_hypo,
+        keep_cc=keep_cc,
+        ctab=ctab,
+        lhminmax=lhminmax,
+        rhminmax=rhminmax,
+        output_usf=output_usf,
+        threads=threads,
+        threads_max=threads_max,
+        threads_max_1=threads_max_1,
+        debug=debug,
+        check_opts=check_opts,
+    )
+    return mri_gtmseg_execute(params, execution)
+
+
+__all__ = [
+    "MRI_GTMSEG_METADATA",
+    "MriGtmsegOutputs",
+    "MriGtmsegParameters",
+    "mri_gtmseg",
+    "mri_gtmseg_params",
+]

niwrap_freesurfer/freesurfer/mri_hausdorff_dist.py

@@ -0,0 +1,257 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_HAUSDORFF_DIST_METADATA = Metadata(
+    id="44ae0e98e23c4f3e6ba34eebfe000f22002a6a97.boutiques",
+    name="mri_hausdorff_dist",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriHausdorffDistParameters = typing.TypedDict('MriHausdorffDistParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_hausdorff_dist"],
+    "vol1": InputPathType,
+    "vol2": InputPathType,
+    "output_text_file": str,
+    "threshold": typing.NotRequired[float | None],
+    "input_file_flag": bool,
+    "blur_sigma": typing.NotRequired[float | None],
+    "max_flag": bool,
+    "label_index": 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_hausdorff_dist": mri_hausdorff_dist_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_hausdorff_dist": mri_hausdorff_dist_outputs,
+    }.get(t)
+
+
+class MriHausdorffDistOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_hausdorff_dist(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_text: OutputPathType
+    """Output text file containing the results of Hausdorff distance
+    calculation"""
+
+
+def mri_hausdorff_dist_params(
+    vol1: InputPathType,
+    vol2: InputPathType,
+    output_text_file: str,
+    threshold: float | None = None,
+    input_file_flag: bool = False,
+    blur_sigma: float | None = None,
+    max_flag: bool = False,
+    label_index: float | None = None,
+) -> MriHausdorffDistParameters:
+    """
+    Build parameters.
+    
+    Args:
+        vol1: First input volume.
+        vol2: Second input volume.
+        output_text_file: Output text file.
+        threshold: Binarize input volumes with given threshold.
+        input_file_flag: Read volumes from an input file (first argument is the\
+            input filename).
+        blur_sigma: Blur the input image with Gaussian of specified sigma.
+        max_flag: Compute the maximum of the minimum distances instead of the\
+            mean.
+        label_index: Use specified label index as the target label.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_hausdorff_dist",
+        "vol1": vol1,
+        "vol2": vol2,
+        "output_text_file": output_text_file,
+        "input_file_flag": input_file_flag,
+        "max_flag": max_flag,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    if blur_sigma is not None:
+        params["blur_sigma"] = blur_sigma
+    if label_index is not None:
+        params["label_index"] = label_index
+    return params
+
+
+def mri_hausdorff_dist_cargs(
+    params: MriHausdorffDistParameters,
+    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_hausdorff_dist")
+    cargs.append(execution.input_file(params.get("vol1")))
+    cargs.append(execution.input_file(params.get("vol2")))
+    cargs.append(params.get("output_text_file"))
+    cargs.append("[BINARIZE_FLAG]")
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-b",
+            str(params.get("threshold"))
+        ])
+    if params.get("input_file_flag"):
+        cargs.append("-F")
+    if params.get("blur_sigma") is not None:
+        cargs.extend([
+            "-g",
+            str(params.get("blur_sigma"))
+        ])
+    if params.get("max_flag"):
+        cargs.append("-max")
+    if params.get("label_index") is not None:
+        cargs.extend([
+            "-l",
+            str(params.get("label_index"))
+        ])
+    return cargs
+
+
+def mri_hausdorff_dist_outputs(
+    params: MriHausdorffDistParameters,
+    execution: Execution,
+) -> MriHausdorffDistOutputs:
+    """
+    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 = MriHausdorffDistOutputs(
+        root=execution.output_file("."),
+        output_text=execution.output_file(params.get("output_text_file")),
+    )
+    return ret
+
+
+def mri_hausdorff_dist_execute(
+    params: MriHausdorffDistParameters,
+    execution: Execution,
+) -> MriHausdorffDistOutputs:
+    """
+    Tool for computing the mean or max of the minimum distances between point sets
+    in 3D volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriHausdorffDistOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_hausdorff_dist_cargs(params, execution)
+    ret = mri_hausdorff_dist_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_hausdorff_dist(
+    vol1: InputPathType,
+    vol2: InputPathType,
+    output_text_file: str,
+    threshold: float | None = None,
+    input_file_flag: bool = False,
+    blur_sigma: float | None = None,
+    max_flag: bool = False,
+    label_index: float | None = None,
+    runner: Runner | None = None,
+) -> MriHausdorffDistOutputs:
+    """
+    Tool for computing the mean or max of the minimum distances between point sets
+    in 3D volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        vol1: First input volume.
+        vol2: Second input volume.
+        output_text_file: Output text file.
+        threshold: Binarize input volumes with given threshold.
+        input_file_flag: Read volumes from an input file (first argument is the\
+            input filename).
+        blur_sigma: Blur the input image with Gaussian of specified sigma.
+        max_flag: Compute the maximum of the minimum distances instead of the\
+            mean.
+        label_index: Use specified label index as the target label.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriHausdorffDistOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_HAUSDORFF_DIST_METADATA)
+    params = mri_hausdorff_dist_params(
+        vol1=vol1,
+        vol2=vol2,
+        output_text_file=output_text_file,
+        threshold=threshold,
+        input_file_flag=input_file_flag,
+        blur_sigma=blur_sigma,
+        max_flag=max_flag,
+        label_index=label_index,
+    )
+    return mri_hausdorff_dist_execute(params, execution)
+
+
+__all__ = [
+    "MRI_HAUSDORFF_DIST_METADATA",
+    "MriHausdorffDistOutputs",
+    "MriHausdorffDistParameters",
+    "mri_hausdorff_dist",
+    "mri_hausdorff_dist_params",
+]