niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_entowm_seg.py

@@ -0,0 +1,478 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_ENTOWM_SEG_METADATA = Metadata(
+    id="40109605e55188f3737d75a9e36af58709374335.boutiques",
+    name="mri_entowm_seg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriEntowmSegParameters = typing.TypedDict('MriEntowmSegParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_entowm_seg"],
+    "input_image": typing.NotRequired[InputPathType | None],
+    "output_segmentation": typing.NotRequired[str | None],
+    "recon_subjects": typing.NotRequired[list[str] | None],
+    "subjects_directory": typing.NotRequired[str | None],
+    "conform": bool,
+    "etiv": bool,
+    "tal": typing.NotRequired[str | None],
+    "write_posteriors": bool,
+    "write_volumes": bool,
+    "write_qa_stats": bool,
+    "exclude_labels": typing.NotRequired[list[str] | None],
+    "keep_ac": bool,
+    "vox_count_volumes": bool,
+    "model_weights": typing.NotRequired[str | None],
+    "color_table": typing.NotRequired[str | None],
+    "population_stats": typing.NotRequired[str | None],
+    "debug": bool,
+    "vmp": bool,
+    "threads": typing.NotRequired[float | None],
+    "seven_tesla": bool,
+    "percentile": typing.NotRequired[float | None],
+    "cuda_device": typing.NotRequired[str | None],
+    "output_base": typing.NotRequired[str | None],
+    "no_cite_sclimbic": bool,
+    "nchannels": 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_entowm_seg": mri_entowm_seg_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_entowm_seg": mri_entowm_seg_outputs,
+    }.get(t)
+
+
+class MriEntowmSegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_entowm_seg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Segmentation output file"""
+    label_posteriors: OutputPathType | None
+    """Label posterior probabilities"""
+    volume_stats: OutputPathType | None
+    """Volume statistics"""
+    qa_stats: OutputPathType | None
+    """Quality assurance statistics"""
+
+
+def mri_entowm_seg_params(
+    input_image: InputPathType | None = None,
+    output_segmentation: str | None = None,
+    recon_subjects: list[str] | None = None,
+    subjects_directory: str | None = None,
+    conform: bool = False,
+    etiv: bool = False,
+    tal: str | None = None,
+    write_posteriors: bool = False,
+    write_volumes: bool = False,
+    write_qa_stats: bool = False,
+    exclude_labels: list[str] | None = None,
+    keep_ac: bool = False,
+    vox_count_volumes: bool = False,
+    model_weights: str | None = None,
+    color_table: str | None = None,
+    population_stats: str | None = None,
+    debug: bool = False,
+    vmp: bool = False,
+    threads: float | None = None,
+    seven_tesla: bool = False,
+    percentile: float | None = None,
+    cuda_device: str | None = None,
+    output_base: str | None = None,
+    no_cite_sclimbic: bool = False,
+    nchannels: float | None = None,
+) -> MriEntowmSegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: T1-weighted image(s) to segment. Can be a path to a single\
+            image or a directory of images.
+        output_segmentation: Segmentation output file or directory (required if\
+            --i is provided).
+        recon_subjects: Process a series of FreeSurfer recon-all subjects,\
+            enables subject-mode.
+        subjects_directory: Set the subjects directory, overrides the\
+            SUBJECTS_DIR env variable.
+        conform: Resample input to 1mm-iso; results will be put back in native\
+            resolution.
+        etiv: Include eTIV in volume stats (enabled by default in subject-mode\
+            and with --tal).
+        tal: Alternative talairach xfm transform for estimating TIV, can be\
+            file or suffix (for multiple inputs).
+        write_posteriors: Save the label posteriors.
+        write_volumes: Save label volume stats (enabled by default in\
+            subject-mode).
+        write_qa_stats: Save QA stats (z and confidence).
+        exclude_labels: List of label IDs to exclude in any output stats files.
+        keep_ac: Explicitly keep anterior commissure in the volume/QA files.
+        vox_count_volumes: Use discrete voxel count for label volumes.
+        model_weights: Alternative model weights to load.
+        color_table: Alternative color lookup table to embed in segmentation.\
+            Must be minimal, including 0, and sorted.
+        population_stats: Alternative population volume stats for QA output.
+        debug: Enable debug logging.
+        vmp: Enable printing of vmpeak at the end.
+        threads: Number of threads to use. Default is 1.
+        seven_tesla: Preprocess 7T images (just sets percentile to 99.9).
+        percentile: Use intensity percentile threshold for normalization.
+        cuda_device: CUDA device for GPU support.
+        output_base: String to use in output file name; default is sclimbic.
+        no_cite_sclimbic: Do not cite sclimbic paper at the end.
+        nchannels: Number of channels.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_entowm_seg",
+        "conform": conform,
+        "etiv": etiv,
+        "write_posteriors": write_posteriors,
+        "write_volumes": write_volumes,
+        "write_qa_stats": write_qa_stats,
+        "keep_ac": keep_ac,
+        "vox_count_volumes": vox_count_volumes,
+        "debug": debug,
+        "vmp": vmp,
+        "seven_tesla": seven_tesla,
+        "no_cite_sclimbic": no_cite_sclimbic,
+    }
+    if input_image is not None:
+        params["input_image"] = input_image
+    if output_segmentation is not None:
+        params["output_segmentation"] = output_segmentation
+    if recon_subjects is not None:
+        params["recon_subjects"] = recon_subjects
+    if subjects_directory is not None:
+        params["subjects_directory"] = subjects_directory
+    if tal is not None:
+        params["tal"] = tal
+    if exclude_labels is not None:
+        params["exclude_labels"] = exclude_labels
+    if model_weights is not None:
+        params["model_weights"] = model_weights
+    if color_table is not None:
+        params["color_table"] = color_table
+    if population_stats is not None:
+        params["population_stats"] = population_stats
+    if threads is not None:
+        params["threads"] = threads
+    if percentile is not None:
+        params["percentile"] = percentile
+    if cuda_device is not None:
+        params["cuda_device"] = cuda_device
+    if output_base is not None:
+        params["output_base"] = output_base
+    if nchannels is not None:
+        params["nchannels"] = nchannels
+    return params
+
+
+def mri_entowm_seg_cargs(
+    params: MriEntowmSegParameters,
+    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_entowm_seg")
+    if params.get("input_image") is not None:
+        cargs.extend([
+            "-i",
+            execution.input_file(params.get("input_image"))
+        ])
+    if params.get("output_segmentation") is not None:
+        cargs.extend([
+            "-o",
+            params.get("output_segmentation")
+        ])
+    if params.get("recon_subjects") is not None:
+        cargs.extend([
+            "-s",
+            *params.get("recon_subjects")
+        ])
+    if params.get("subjects_directory") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_directory")
+        ])
+    if params.get("conform"):
+        cargs.append("--conform")
+    if params.get("etiv"):
+        cargs.append("--etiv")
+    if params.get("tal") is not None:
+        cargs.extend([
+            "--tal",
+            params.get("tal")
+        ])
+    if params.get("write_posteriors"):
+        cargs.append("--write_posteriors")
+    if params.get("write_volumes"):
+        cargs.append("--write_volumes")
+    if params.get("write_qa_stats"):
+        cargs.append("--write_qa_stats")
+    if params.get("exclude_labels") is not None:
+        cargs.extend([
+            "--exclude",
+            *params.get("exclude_labels")
+        ])
+    if params.get("keep_ac"):
+        cargs.append("--keep_ac")
+    if params.get("vox_count_volumes"):
+        cargs.append("--vox-count-volumes")
+    if params.get("model_weights") is not None:
+        cargs.extend([
+            "--model",
+            params.get("model_weights")
+        ])
+    if params.get("color_table") is not None:
+        cargs.extend([
+            "--ctab",
+            params.get("color_table")
+        ])
+    if params.get("population_stats") is not None:
+        cargs.extend([
+            "--population-stats",
+            params.get("population_stats")
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("vmp"):
+        cargs.append("--vmp")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("seven_tesla"):
+        cargs.append("--7T")
+    if params.get("percentile") is not None:
+        cargs.extend([
+            "--percentile",
+            str(params.get("percentile"))
+        ])
+    if params.get("cuda_device") is not None:
+        cargs.extend([
+            "--cuda-device",
+            params.get("cuda_device")
+        ])
+    if params.get("output_base") is not None:
+        cargs.extend([
+            "--output-base",
+            params.get("output_base")
+        ])
+    if params.get("no_cite_sclimbic"):
+        cargs.append("--no-cite-sclimbic")
+    if params.get("nchannels") is not None:
+        cargs.extend([
+            "--nchannels",
+            str(params.get("nchannels"))
+        ])
+    return cargs
+
+
+def mri_entowm_seg_outputs(
+    params: MriEntowmSegParameters,
+    execution: Execution,
+) -> MriEntowmSegOutputs:
+    """
+    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 = MriEntowmSegOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_segmentation")) if (params.get("output_segmentation") is not None) else None,
+        label_posteriors=execution.output_file(params.get("output_base") + "_posterior.mgz") if (params.get("output_base") is not None) else None,
+        volume_stats=execution.output_file(params.get("output_base") + "_volumes.txt") if (params.get("output_base") is not None) else None,
+        qa_stats=execution.output_file(params.get("output_base") + "_qa_stats.txt") if (params.get("output_base") is not None) else None,
+    )
+    return ret
+
+
+def mri_entowm_seg_execute(
+    params: MriEntowmSegParameters,
+    execution: Execution,
+) -> MriEntowmSegOutputs:
+    """
+    Segment white matter near gyrus ambiens entorhinal cortex using a deep learning
+    model.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriEntowmSegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_entowm_seg_cargs(params, execution)
+    ret = mri_entowm_seg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_entowm_seg(
+    input_image: InputPathType | None = None,
+    output_segmentation: str | None = None,
+    recon_subjects: list[str] | None = None,
+    subjects_directory: str | None = None,
+    conform: bool = False,
+    etiv: bool = False,
+    tal: str | None = None,
+    write_posteriors: bool = False,
+    write_volumes: bool = False,
+    write_qa_stats: bool = False,
+    exclude_labels: list[str] | None = None,
+    keep_ac: bool = False,
+    vox_count_volumes: bool = False,
+    model_weights: str | None = None,
+    color_table: str | None = None,
+    population_stats: str | None = None,
+    debug: bool = False,
+    vmp: bool = False,
+    threads: float | None = None,
+    seven_tesla: bool = False,
+    percentile: float | None = None,
+    cuda_device: str | None = None,
+    output_base: str | None = None,
+    no_cite_sclimbic: bool = False,
+    nchannels: float | None = None,
+    runner: Runner | None = None,
+) -> MriEntowmSegOutputs:
+    """
+    Segment white matter near gyrus ambiens entorhinal cortex using a deep learning
+    model.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: T1-weighted image(s) to segment. Can be a path to a single\
+            image or a directory of images.
+        output_segmentation: Segmentation output file or directory (required if\
+            --i is provided).
+        recon_subjects: Process a series of FreeSurfer recon-all subjects,\
+            enables subject-mode.
+        subjects_directory: Set the subjects directory, overrides the\
+            SUBJECTS_DIR env variable.
+        conform: Resample input to 1mm-iso; results will be put back in native\
+            resolution.
+        etiv: Include eTIV in volume stats (enabled by default in subject-mode\
+            and with --tal).
+        tal: Alternative talairach xfm transform for estimating TIV, can be\
+            file or suffix (for multiple inputs).
+        write_posteriors: Save the label posteriors.
+        write_volumes: Save label volume stats (enabled by default in\
+            subject-mode).
+        write_qa_stats: Save QA stats (z and confidence).
+        exclude_labels: List of label IDs to exclude in any output stats files.
+        keep_ac: Explicitly keep anterior commissure in the volume/QA files.
+        vox_count_volumes: Use discrete voxel count for label volumes.
+        model_weights: Alternative model weights to load.
+        color_table: Alternative color lookup table to embed in segmentation.\
+            Must be minimal, including 0, and sorted.
+        population_stats: Alternative population volume stats for QA output.
+        debug: Enable debug logging.
+        vmp: Enable printing of vmpeak at the end.
+        threads: Number of threads to use. Default is 1.
+        seven_tesla: Preprocess 7T images (just sets percentile to 99.9).
+        percentile: Use intensity percentile threshold for normalization.
+        cuda_device: CUDA device for GPU support.
+        output_base: String to use in output file name; default is sclimbic.
+        no_cite_sclimbic: Do not cite sclimbic paper at the end.
+        nchannels: Number of channels.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriEntowmSegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_ENTOWM_SEG_METADATA)
+    params = mri_entowm_seg_params(
+        input_image=input_image,
+        output_segmentation=output_segmentation,
+        recon_subjects=recon_subjects,
+        subjects_directory=subjects_directory,
+        conform=conform,
+        etiv=etiv,
+        tal=tal,
+        write_posteriors=write_posteriors,
+        write_volumes=write_volumes,
+        write_qa_stats=write_qa_stats,
+        exclude_labels=exclude_labels,
+        keep_ac=keep_ac,
+        vox_count_volumes=vox_count_volumes,
+        model_weights=model_weights,
+        color_table=color_table,
+        population_stats=population_stats,
+        debug=debug,
+        vmp=vmp,
+        threads=threads,
+        seven_tesla=seven_tesla,
+        percentile=percentile,
+        cuda_device=cuda_device,
+        output_base=output_base,
+        no_cite_sclimbic=no_cite_sclimbic,
+        nchannels=nchannels,
+    )
+    return mri_entowm_seg_execute(params, execution)
+
+
+__all__ = [
+    "MRI_ENTOWM_SEG_METADATA",
+    "MriEntowmSegOutputs",
+    "MriEntowmSegParameters",
+    "mri_entowm_seg",
+    "mri_entowm_seg_params",
+]

niwrap_freesurfer/freesurfer/mri_evaluate_morph.py

@@ -0,0 +1,194 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EVALUATE_MORPH_METADATA = Metadata(
+    id="80d2aca899795eab8a40cb4bb8b3d34e4bf9970e.boutiques",
+    name="mri_evaluate_morph",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriEvaluateMorphParameters = typing.TypedDict('MriEvaluateMorphParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_evaluate_morph"],
+    "xform_name": InputPathType,
+    "segmentation_files": list[InputPathType],
+    "output_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 {
+        "mri_evaluate_morph": mri_evaluate_morph_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_evaluate_morph": mri_evaluate_morph_outputs,
+    }.get(t)
+
+
+class MriEvaluateMorphOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_evaluate_morph(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_overlap_file: OutputPathType
+    """The output file containing overlap results."""
+
+
+def mri_evaluate_morph_params(
+    xform_name: InputPathType,
+    segmentation_files: list[InputPathType],
+    output_file: str,
+) -> MriEvaluateMorphParameters:
+    """
+    Build parameters.
+    
+    Args:
+        xform_name: Transformation file name.
+        segmentation_files: Input segmentation files.
+        output_file: Output file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_evaluate_morph",
+        "xform_name": xform_name,
+        "segmentation_files": segmentation_files,
+        "output_file": output_file,
+    }
+    return params
+
+
+def mri_evaluate_morph_cargs(
+    params: MriEvaluateMorphParameters,
+    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_evaluate_morph")
+    cargs.append(execution.input_file(params.get("xform_name")))
+    cargs.extend([execution.input_file(f) for f in params.get("segmentation_files")])
+    cargs.append(params.get("output_file"))
+    return cargs
+
+
+def mri_evaluate_morph_outputs(
+    params: MriEvaluateMorphParameters,
+    execution: Execution,
+) -> MriEvaluateMorphOutputs:
+    """
+    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 = MriEvaluateMorphOutputs(
+        root=execution.output_file("."),
+        output_overlap_file=execution.output_file(params.get("output_file")),
+    )
+    return ret
+
+
+def mri_evaluate_morph_execute(
+    params: MriEvaluateMorphParameters,
+    execution: Execution,
+) -> MriEvaluateMorphOutputs:
+    """
+    This program computes the overlap of a set of segmentations for a given morph
+    using an xform file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriEvaluateMorphOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_evaluate_morph_cargs(params, execution)
+    ret = mri_evaluate_morph_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_evaluate_morph(
+    xform_name: InputPathType,
+    segmentation_files: list[InputPathType],
+    output_file: str,
+    runner: Runner | None = None,
+) -> MriEvaluateMorphOutputs:
+    """
+    This program computes the overlap of a set of segmentations for a given morph
+    using an xform file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        xform_name: Transformation file name.
+        segmentation_files: Input segmentation files.
+        output_file: Output file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriEvaluateMorphOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EVALUATE_MORPH_METADATA)
+    params = mri_evaluate_morph_params(
+        xform_name=xform_name,
+        segmentation_files=segmentation_files,
+        output_file=output_file,
+    )
+    return mri_evaluate_morph_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EVALUATE_MORPH_METADATA",
+    "MriEvaluateMorphOutputs",
+    "MriEvaluateMorphParameters",
+    "mri_evaluate_morph",
+    "mri_evaluate_morph_params",
+]