niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_fill.py

@@ -0,0 +1,392 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_FILL_METADATA = Metadata(
+    id="45567bfdadd532485f2ed2b4fee5ffc3e7f9d609.boutiques",
+    name="mri_fill",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriFillParameters = typing.TypedDict('MriFillParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_fill"],
+    "input_mr_dir": str,
+    "output_mr_dir": str,
+    "threshold": typing.NotRequired[float | None],
+    "xform_name": typing.NotRequired[str | None],
+    "segmentation_file": typing.NotRequired[InputPathType | None],
+    "atlas_file": typing.NotRequired[InputPathType | None],
+    "fill_ven": bool,
+    "seed_cc_tal": typing.NotRequired[list[float] | None],
+    "seed_pons_tal": typing.NotRequired[list[float] | None],
+    "seed_lh_tal": typing.NotRequired[list[float] | None],
+    "seed_rh_tal": typing.NotRequired[list[float] | None],
+    "seed_cc_vox": typing.NotRequired[list[float] | None],
+    "seed_pons_vox": typing.NotRequired[list[float] | None],
+    "auto_man_files": typing.NotRequired[list[str] | None],
+    "no_auto_man": bool,
+    "pointset_args": typing.NotRequired[list[str] | None],
+    "ctab_file": typing.NotRequired[InputPathType | 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_fill": mri_fill_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_fill": mri_fill_outputs,
+    }.get(t)
+
+
+class MriFillOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_fill(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    filled_volume: OutputPathType
+    """The filled volume for the cortical reconstruction, used for subsequent
+    surface tessellation"""
+
+
+def mri_fill_params(
+    input_mr_dir: str,
+    output_mr_dir: str,
+    threshold: float | None = None,
+    xform_name: str | None = None,
+    segmentation_file: InputPathType | None = None,
+    atlas_file: InputPathType | None = None,
+    fill_ven: bool = False,
+    seed_cc_tal: list[float] | None = None,
+    seed_pons_tal: list[float] | None = None,
+    seed_lh_tal: list[float] | None = None,
+    seed_rh_tal: list[float] | None = None,
+    seed_cc_vox: list[float] | None = None,
+    seed_pons_vox: list[float] | None = None,
+    auto_man_files: list[str] | None = None,
+    no_auto_man: bool = False,
+    pointset_args: list[str] | None = None,
+    ctab_file: InputPathType | None = None,
+) -> MriFillParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_mr_dir: Input MR directory.
+        output_mr_dir: Output MR directory.
+        threshold: Specify fill_holes threshold (default=1).
+        xform_name: Use xform dst offset to get an accurate Talairach volume.
+        segmentation_file: ASEG volume used to perform fill.
+        atlas_file: Specify atlas to use for auto-filling.
+        fill_ven: Fill ventricles.
+        seed_cc_tal: Talairach coords of the seed for the corpus callosum\
+            (three numerical values required).
+        seed_pons_tal: Talairach coords of the seed for the pons (three\
+            numerical values required).
+        seed_lh_tal: Talairach coords of the white matter seed for the left\
+            hemisphere (three numerical values required).
+        seed_rh_tal: Talairach coords of the white matter seed for the right\
+            hemisphere (three numerical values required).
+        seed_cc_vox: Voxel coords of the seed for the corpus callosum (three\
+            numerical values required).
+        seed_pons_vox: Voxel coords of the seed for the pons (three numerical\
+            values required).
+        auto_man_files: Get edits based on the difference between auto and man\
+            and apply to the output.
+        no_auto_man: Turns off the -auto-man option.
+        pointset_args: Stand-alone option: takes one or more pointsets and\
+            fills in all the voxels that intersect lines connecting any two points\
+            within a given point set.
+        ctab_file: Embed color table in the output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_fill",
+        "input_mr_dir": input_mr_dir,
+        "output_mr_dir": output_mr_dir,
+        "fill_ven": fill_ven,
+        "no_auto_man": no_auto_man,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    if xform_name is not None:
+        params["xform_name"] = xform_name
+    if segmentation_file is not None:
+        params["segmentation_file"] = segmentation_file
+    if atlas_file is not None:
+        params["atlas_file"] = atlas_file
+    if seed_cc_tal is not None:
+        params["seed_cc_tal"] = seed_cc_tal
+    if seed_pons_tal is not None:
+        params["seed_pons_tal"] = seed_pons_tal
+    if seed_lh_tal is not None:
+        params["seed_lh_tal"] = seed_lh_tal
+    if seed_rh_tal is not None:
+        params["seed_rh_tal"] = seed_rh_tal
+    if seed_cc_vox is not None:
+        params["seed_cc_vox"] = seed_cc_vox
+    if seed_pons_vox is not None:
+        params["seed_pons_vox"] = seed_pons_vox
+    if auto_man_files is not None:
+        params["auto_man_files"] = auto_man_files
+    if pointset_args is not None:
+        params["pointset_args"] = pointset_args
+    if ctab_file is not None:
+        params["ctab_file"] = ctab_file
+    return params
+
+
+def mri_fill_cargs(
+    params: MriFillParameters,
+    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_fill")
+    cargs.append(params.get("input_mr_dir"))
+    cargs.append(params.get("output_mr_dir"))
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-T",
+            str(params.get("threshold"))
+        ])
+    if params.get("xform_name") is not None:
+        cargs.extend([
+            "-xform",
+            params.get("xform_name")
+        ])
+    if params.get("segmentation_file") is not None:
+        cargs.extend([
+            "-segmentation",
+            execution.input_file(params.get("segmentation_file"))
+        ])
+    if params.get("atlas_file") is not None:
+        cargs.extend([
+            "-atlas",
+            execution.input_file(params.get("atlas_file"))
+        ])
+    if params.get("fill_ven"):
+        cargs.append("-fillven")
+    if params.get("seed_cc_tal") is not None:
+        cargs.extend([
+            "-C",
+            *map(str, params.get("seed_cc_tal"))
+        ])
+    if params.get("seed_pons_tal") is not None:
+        cargs.extend([
+            "-P",
+            *map(str, params.get("seed_pons_tal"))
+        ])
+    if params.get("seed_lh_tal") is not None:
+        cargs.extend([
+            "-lh",
+            *map(str, params.get("seed_lh_tal"))
+        ])
+    if params.get("seed_rh_tal") is not None:
+        cargs.extend([
+            "-rh",
+            *map(str, params.get("seed_rh_tal"))
+        ])
+    if params.get("seed_cc_vox") is not None:
+        cargs.extend([
+            "-CV",
+            *map(str, params.get("seed_cc_vox"))
+        ])
+    if params.get("seed_pons_vox") is not None:
+        cargs.extend([
+            "-PV",
+            *map(str, params.get("seed_pons_vox"))
+        ])
+    if params.get("auto_man_files") is not None:
+        cargs.extend([
+            "-auto-man",
+            *params.get("auto_man_files")
+        ])
+    if params.get("no_auto_man"):
+        cargs.append("-no-auto-man")
+    if params.get("pointset_args") is not None:
+        cargs.extend([
+            "-pointset",
+            *params.get("pointset_args")
+        ])
+    if params.get("ctab_file") is not None:
+        cargs.extend([
+            "-ctab",
+            execution.input_file(params.get("ctab_file"))
+        ])
+    return cargs
+
+
+def mri_fill_outputs(
+    params: MriFillParameters,
+    execution: Execution,
+) -> MriFillOutputs:
+    """
+    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 = MriFillOutputs(
+        root=execution.output_file("."),
+        filled_volume=execution.output_file(params.get("output_mr_dir") + "/filled"),
+    )
+    return ret
+
+
+def mri_fill_execute(
+    params: MriFillParameters,
+    execution: Execution,
+) -> MriFillOutputs:
+    """
+    Tool for creating hemispheric cutting planes and filling white matter for
+    surface tessellation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriFillOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_fill_cargs(params, execution)
+    ret = mri_fill_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_fill(
+    input_mr_dir: str,
+    output_mr_dir: str,
+    threshold: float | None = None,
+    xform_name: str | None = None,
+    segmentation_file: InputPathType | None = None,
+    atlas_file: InputPathType | None = None,
+    fill_ven: bool = False,
+    seed_cc_tal: list[float] | None = None,
+    seed_pons_tal: list[float] | None = None,
+    seed_lh_tal: list[float] | None = None,
+    seed_rh_tal: list[float] | None = None,
+    seed_cc_vox: list[float] | None = None,
+    seed_pons_vox: list[float] | None = None,
+    auto_man_files: list[str] | None = None,
+    no_auto_man: bool = False,
+    pointset_args: list[str] | None = None,
+    ctab_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriFillOutputs:
+    """
+    Tool for creating hemispheric cutting planes and filling white matter for
+    surface tessellation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_mr_dir: Input MR directory.
+        output_mr_dir: Output MR directory.
+        threshold: Specify fill_holes threshold (default=1).
+        xform_name: Use xform dst offset to get an accurate Talairach volume.
+        segmentation_file: ASEG volume used to perform fill.
+        atlas_file: Specify atlas to use for auto-filling.
+        fill_ven: Fill ventricles.
+        seed_cc_tal: Talairach coords of the seed for the corpus callosum\
+            (three numerical values required).
+        seed_pons_tal: Talairach coords of the seed for the pons (three\
+            numerical values required).
+        seed_lh_tal: Talairach coords of the white matter seed for the left\
+            hemisphere (three numerical values required).
+        seed_rh_tal: Talairach coords of the white matter seed for the right\
+            hemisphere (three numerical values required).
+        seed_cc_vox: Voxel coords of the seed for the corpus callosum (three\
+            numerical values required).
+        seed_pons_vox: Voxel coords of the seed for the pons (three numerical\
+            values required).
+        auto_man_files: Get edits based on the difference between auto and man\
+            and apply to the output.
+        no_auto_man: Turns off the -auto-man option.
+        pointset_args: Stand-alone option: takes one or more pointsets and\
+            fills in all the voxels that intersect lines connecting any two points\
+            within a given point set.
+        ctab_file: Embed color table in the output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriFillOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FILL_METADATA)
+    params = mri_fill_params(
+        input_mr_dir=input_mr_dir,
+        output_mr_dir=output_mr_dir,
+        threshold=threshold,
+        xform_name=xform_name,
+        segmentation_file=segmentation_file,
+        atlas_file=atlas_file,
+        fill_ven=fill_ven,
+        seed_cc_tal=seed_cc_tal,
+        seed_pons_tal=seed_pons_tal,
+        seed_lh_tal=seed_lh_tal,
+        seed_rh_tal=seed_rh_tal,
+        seed_cc_vox=seed_cc_vox,
+        seed_pons_vox=seed_pons_vox,
+        auto_man_files=auto_man_files,
+        no_auto_man=no_auto_man,
+        pointset_args=pointset_args,
+        ctab_file=ctab_file,
+    )
+    return mri_fill_execute(params, execution)
+
+
+__all__ = [
+    "MRI_FILL_METADATA",
+    "MriFillOutputs",
+    "MriFillParameters",
+    "mri_fill",
+    "mri_fill_params",
+]

niwrap_freesurfer/freesurfer/mri_fit_bias.py

@@ -0,0 +1,313 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_FIT_BIAS_METADATA = Metadata(
+    id="5cfc424aa0f54308ca89e9fae020adbc05a2f8ca.boutiques",
+    name="mri_fit_bias",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriFitBiasParameters = typing.TypedDict('MriFitBiasParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_fit_bias"],
+    "inputvol": InputPathType,
+    "lpf_cutoff": typing.NotRequired[float | None],
+    "segvol": InputPathType,
+    "maskvol": InputPathType,
+    "outvol": str,
+    "biasfield": str,
+    "dctvol": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "nerode": typing.NotRequired[float | None],
+    "nthreads": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": 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_fit_bias": mri_fit_bias_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_fit_bias": mri_fit_bias_outputs,
+    }.get(t)
+
+
+class MriFitBiasOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_fit_bias(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corrected_output: OutputPathType
+    """Bias corrected output volume"""
+    generated_bias_field: OutputPathType
+    """Generated bias field"""
+
+
+def mri_fit_bias_params(
+    inputvol: InputPathType,
+    segvol: InputPathType,
+    maskvol: InputPathType,
+    outvol: str,
+    biasfield: str,
+    lpf_cutoff: float | None = 23.0,
+    dctvol: str | None = None,
+    threshold: float | None = None,
+    nerode: float | None = 1,
+    nthreads: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+) -> MriFitBiasParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inputvol: Input volume for intensity normalization.
+        segvol: Segmentation volume to define WM and Cortex (e.g.,\
+            aseg.presurf.mgz).
+        maskvol: Mask volume; zero everything outside of the mask (e.g.,\
+            brainmask.mgz).
+        outvol: Bias corrected output volume.
+        biasfield: Output bias field.
+        lpf_cutoff: Low-pass filter cutoff in mm (default is 23.000000).
+        dctvol: DCT fields file for debugging.
+        threshold: Mask out anything <= threshold value.
+        nerode: 3D erode segmentation by n steps (default is 1).
+        nthreads: Number of threads to use.
+        debug: Turn on debugging mode.
+        checkopts: Don't run anything, just check options and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_fit_bias",
+        "inputvol": inputvol,
+        "segvol": segvol,
+        "maskvol": maskvol,
+        "outvol": outvol,
+        "biasfield": biasfield,
+        "debug": debug,
+        "checkopts": checkopts,
+    }
+    if lpf_cutoff is not None:
+        params["lpf_cutoff"] = lpf_cutoff
+    if dctvol is not None:
+        params["dctvol"] = dctvol
+    if threshold is not None:
+        params["threshold"] = threshold
+    if nerode is not None:
+        params["nerode"] = nerode
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    return params
+
+
+def mri_fit_bias_cargs(
+    params: MriFitBiasParameters,
+    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_fit_bias")
+    cargs.extend([
+        "--i",
+        execution.input_file(params.get("inputvol"))
+    ])
+    if params.get("lpf_cutoff") is not None:
+        cargs.extend([
+            "--cutoff",
+            str(params.get("lpf_cutoff"))
+        ])
+    cargs.extend([
+        "--seg",
+        execution.input_file(params.get("segvol"))
+    ])
+    cargs.extend([
+        "--mask",
+        execution.input_file(params.get("maskvol"))
+    ])
+    cargs.extend([
+        "--o",
+        params.get("outvol")
+    ])
+    cargs.extend([
+        "--bias",
+        params.get("biasfield")
+    ])
+    if params.get("dctvol") is not None:
+        cargs.extend([
+            "--dct",
+            params.get("dctvol")
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "--thresh",
+            str(params.get("threshold"))
+        ])
+    if params.get("nerode") is not None:
+        cargs.extend([
+            "--erode",
+            str(params.get("nerode"))
+        ])
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    return cargs
+
+
+def mri_fit_bias_outputs(
+    params: MriFitBiasParameters,
+    execution: Execution,
+) -> MriFitBiasOutputs:
+    """
+    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 = MriFitBiasOutputs(
+        root=execution.output_file("."),
+        corrected_output=execution.output_file(params.get("outvol")),
+        generated_bias_field=execution.output_file(params.get("biasfield")),
+    )
+    return ret
+
+
+def mri_fit_bias_execute(
+    params: MriFitBiasParameters,
+    execution: Execution,
+) -> MriFitBiasOutputs:
+    """
+    A tool for intensity normalization and bias correction in MRI images.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriFitBiasOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_fit_bias_cargs(params, execution)
+    ret = mri_fit_bias_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_fit_bias(
+    inputvol: InputPathType,
+    segvol: InputPathType,
+    maskvol: InputPathType,
+    outvol: str,
+    biasfield: str,
+    lpf_cutoff: float | None = 23.0,
+    dctvol: str | None = None,
+    threshold: float | None = None,
+    nerode: float | None = 1,
+    nthreads: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    runner: Runner | None = None,
+) -> MriFitBiasOutputs:
+    """
+    A tool for intensity normalization and bias correction in MRI images.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        inputvol: Input volume for intensity normalization.
+        segvol: Segmentation volume to define WM and Cortex (e.g.,\
+            aseg.presurf.mgz).
+        maskvol: Mask volume; zero everything outside of the mask (e.g.,\
+            brainmask.mgz).
+        outvol: Bias corrected output volume.
+        biasfield: Output bias field.
+        lpf_cutoff: Low-pass filter cutoff in mm (default is 23.000000).
+        dctvol: DCT fields file for debugging.
+        threshold: Mask out anything <= threshold value.
+        nerode: 3D erode segmentation by n steps (default is 1).
+        nthreads: Number of threads to use.
+        debug: Turn on debugging mode.
+        checkopts: Don't run anything, just check options and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriFitBiasOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FIT_BIAS_METADATA)
+    params = mri_fit_bias_params(
+        inputvol=inputvol,
+        lpf_cutoff=lpf_cutoff,
+        segvol=segvol,
+        maskvol=maskvol,
+        outvol=outvol,
+        biasfield=biasfield,
+        dctvol=dctvol,
+        threshold=threshold,
+        nerode=nerode,
+        nthreads=nthreads,
+        debug=debug,
+        checkopts=checkopts,
+    )
+    return mri_fit_bias_execute(params, execution)
+
+
+__all__ = [
+    "MRI_FIT_BIAS_METADATA",
+    "MriFitBiasOutputs",
+    "MriFitBiasParameters",
+    "mri_fit_bias",
+    "mri_fit_bias_params",
+]