niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/make_average_surface.py

@@ -0,0 +1,399 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_AVERAGE_SURFACE_METADATA = Metadata(
+    id="f27d1881cb0ec462784332cf8519b93ee957748e.boutiques",
+    name="make_average_surface",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MakeAverageSurfaceParameters = typing.TypedDict('MakeAverageSurfaceParameters', {
+    "__STYX_TYPE__": typing.Literal["make_average_surface"],
+    "subjects": list[str],
+    "fsgd_file": typing.NotRequired[InputPathType | None],
+    "average_subject_name": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "sd_out_dir": typing.NotRequired[str | None],
+    "transform_file": typing.NotRequired[str | None],
+    "icosahedron_number": typing.NotRequired[float | None],
+    "surf_reg": typing.NotRequired[str | None],
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "force": bool,
+    "annot_template": bool,
+    "template_only": bool,
+    "no_template_only": bool,
+    "no_annot": bool,
+    "no_cortex_label": bool,
+    "annot_list": typing.NotRequired[list[str] | None],
+    "meas_list": typing.NotRequired[list[str] | None],
+    "no_surf2surf": bool,
+    "no_symlink": bool,
+    "version": bool,
+    "echo": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "make_average_surface": make_average_surface_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 MakeAverageSurfaceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_average_surface(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def make_average_surface_params(
+    subjects: list[str],
+    fsgd_file: InputPathType | None = None,
+    average_subject_name: str | None = "average",
+    subjects_dir: str | None = None,
+    sd_out_dir: str | None = None,
+    transform_file: str | None = None,
+    icosahedron_number: float | None = 7,
+    surf_reg: str | None = None,
+    left_hemi: bool = False,
+    right_hemi: bool = False,
+    force: bool = False,
+    annot_template: bool = False,
+    template_only: bool = False,
+    no_template_only: bool = False,
+    no_annot: bool = False,
+    no_cortex_label: bool = False,
+    annot_list: list[str] | None = None,
+    meas_list: list[str] | None = None,
+    no_surf2surf: bool = False,
+    no_symlink: bool = False,
+    version: bool = False,
+    echo: bool = False,
+) -> MakeAverageSurfaceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects: List of subject names.
+        fsgd_file: File from which to get the subject list.
+        average_subject_name: Average subject name.
+        subjects_dir: Directory for SUBJECTS_DIR (if different from the\
+            environment variable).
+        sd_out_dir: Directory to put output data.
+        transform_file: Filename of the transform file.
+        icosahedron_number: Specify icosahedron number.
+        surf_reg: Alternative registration surface name.
+        left_hemi: Only process the left hemisphere.
+        right_hemi: Only process the right hemisphere.
+        force: Overwrite existing average subject data.
+        annot_template: Use annotation when making tif.
+        template_only: Useful when creating iterative atlases.
+        no_template_only: Turns off --template-only.
+        no_annot: Do not create average annotations.
+        no_cortex_label: Do not create ?h.cortex.label.
+        annot_list: List of annotations to use.
+        meas_list: List of measurements to use.
+        no_surf2surf: Use old parametric surface method.
+        no_symlink: Do not use symbolic links, just copy files.
+        version: Script version information.
+        echo: Enable command echo for debugging.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_average_surface",
+        "subjects": subjects,
+        "left_hemi": left_hemi,
+        "right_hemi": right_hemi,
+        "force": force,
+        "annot_template": annot_template,
+        "template_only": template_only,
+        "no_template_only": no_template_only,
+        "no_annot": no_annot,
+        "no_cortex_label": no_cortex_label,
+        "no_surf2surf": no_surf2surf,
+        "no_symlink": no_symlink,
+        "version": version,
+        "echo": echo,
+    }
+    if fsgd_file is not None:
+        params["fsgd_file"] = fsgd_file
+    if average_subject_name is not None:
+        params["average_subject_name"] = average_subject_name
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if sd_out_dir is not None:
+        params["sd_out_dir"] = sd_out_dir
+    if transform_file is not None:
+        params["transform_file"] = transform_file
+    if icosahedron_number is not None:
+        params["icosahedron_number"] = icosahedron_number
+    if surf_reg is not None:
+        params["surf_reg"] = surf_reg
+    if annot_list is not None:
+        params["annot_list"] = annot_list
+    if meas_list is not None:
+        params["meas_list"] = meas_list
+    return params
+
+
+def make_average_surface_cargs(
+    params: MakeAverageSurfaceParameters,
+    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("make_average_surface")
+    cargs.extend(params.get("subjects"))
+    if params.get("fsgd_file") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("fsgd_file"))
+        ])
+    if params.get("average_subject_name") is not None:
+        cargs.extend([
+            "--out",
+            params.get("average_subject_name")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sdir",
+            params.get("subjects_dir")
+        ])
+    if params.get("sd_out_dir") is not None:
+        cargs.extend([
+            "--sd-out",
+            params.get("sd_out_dir")
+        ])
+    if params.get("transform_file") is not None:
+        cargs.extend([
+            "--xform",
+            params.get("transform_file")
+        ])
+    if params.get("icosahedron_number") is not None:
+        cargs.extend([
+            "--ico",
+            str(params.get("icosahedron_number"))
+        ])
+    if params.get("surf_reg") is not None:
+        cargs.extend([
+            "--surf-reg",
+            params.get("surf_reg")
+        ])
+    if params.get("left_hemi"):
+        cargs.append("--lh")
+    if params.get("right_hemi"):
+        cargs.append("--rh")
+    if params.get("force"):
+        cargs.append("--force")
+    if params.get("annot_template"):
+        cargs.append("--annot-template")
+    if params.get("template_only"):
+        cargs.append("--template-only")
+    if params.get("no_template_only"):
+        cargs.append("--no-template-only")
+    if params.get("no_annot"):
+        cargs.append("--no-annot")
+    if params.get("no_cortex_label"):
+        cargs.append("--no-cortex-label")
+    if params.get("annot_list") is not None:
+        cargs.extend([
+            "--annot",
+            *params.get("annot_list")
+        ])
+    if params.get("meas_list") is not None:
+        cargs.extend([
+            "--meas",
+            *params.get("meas_list")
+        ])
+    if params.get("no_surf2surf"):
+        cargs.append("--no-surf2surf")
+    if params.get("no_symlink"):
+        cargs.append("--no-symlink")
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("echo"):
+        cargs.append("--echo")
+    return cargs
+
+
+def make_average_surface_outputs(
+    params: MakeAverageSurfaceParameters,
+    execution: Execution,
+) -> MakeAverageSurfaceOutputs:
+    """
+    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 = MakeAverageSurfaceOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def make_average_surface_execute(
+    params: MakeAverageSurfaceParameters,
+    execution: Execution,
+) -> MakeAverageSurfaceOutputs:
+    """
+    Creates average surfaces and curvatures from a set of subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeAverageSurfaceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_average_surface_cargs(params, execution)
+    ret = make_average_surface_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_average_surface(
+    subjects: list[str],
+    fsgd_file: InputPathType | None = None,
+    average_subject_name: str | None = "average",
+    subjects_dir: str | None = None,
+    sd_out_dir: str | None = None,
+    transform_file: str | None = None,
+    icosahedron_number: float | None = 7,
+    surf_reg: str | None = None,
+    left_hemi: bool = False,
+    right_hemi: bool = False,
+    force: bool = False,
+    annot_template: bool = False,
+    template_only: bool = False,
+    no_template_only: bool = False,
+    no_annot: bool = False,
+    no_cortex_label: bool = False,
+    annot_list: list[str] | None = None,
+    meas_list: list[str] | None = None,
+    no_surf2surf: bool = False,
+    no_symlink: bool = False,
+    version: bool = False,
+    echo: bool = False,
+    runner: Runner | None = None,
+) -> MakeAverageSurfaceOutputs:
+    """
+    Creates average surfaces and curvatures from a set of subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects: List of subject names.
+        fsgd_file: File from which to get the subject list.
+        average_subject_name: Average subject name.
+        subjects_dir: Directory for SUBJECTS_DIR (if different from the\
+            environment variable).
+        sd_out_dir: Directory to put output data.
+        transform_file: Filename of the transform file.
+        icosahedron_number: Specify icosahedron number.
+        surf_reg: Alternative registration surface name.
+        left_hemi: Only process the left hemisphere.
+        right_hemi: Only process the right hemisphere.
+        force: Overwrite existing average subject data.
+        annot_template: Use annotation when making tif.
+        template_only: Useful when creating iterative atlases.
+        no_template_only: Turns off --template-only.
+        no_annot: Do not create average annotations.
+        no_cortex_label: Do not create ?h.cortex.label.
+        annot_list: List of annotations to use.
+        meas_list: List of measurements to use.
+        no_surf2surf: Use old parametric surface method.
+        no_symlink: Do not use symbolic links, just copy files.
+        version: Script version information.
+        echo: Enable command echo for debugging.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeAverageSurfaceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_AVERAGE_SURFACE_METADATA)
+    params = make_average_surface_params(
+        subjects=subjects,
+        fsgd_file=fsgd_file,
+        average_subject_name=average_subject_name,
+        subjects_dir=subjects_dir,
+        sd_out_dir=sd_out_dir,
+        transform_file=transform_file,
+        icosahedron_number=icosahedron_number,
+        surf_reg=surf_reg,
+        left_hemi=left_hemi,
+        right_hemi=right_hemi,
+        force=force,
+        annot_template=annot_template,
+        template_only=template_only,
+        no_template_only=no_template_only,
+        no_annot=no_annot,
+        no_cortex_label=no_cortex_label,
+        annot_list=annot_list,
+        meas_list=meas_list,
+        no_surf2surf=no_surf2surf,
+        no_symlink=no_symlink,
+        version=version,
+        echo=echo,
+    )
+    return make_average_surface_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_AVERAGE_SURFACE_METADATA",
+    "MakeAverageSurfaceOutputs",
+    "MakeAverageSurfaceParameters",
+    "make_average_surface",
+    "make_average_surface_params",
+]

niwrap_freesurfer/freesurfer/make_average_volume.py

@@ -0,0 +1,309 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_AVERAGE_VOLUME_METADATA = Metadata(
+    id="52d00009c5f5db471f13423dea8699f07efa357d.boutiques",
+    name="make_average_volume",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MakeAverageVolumeParameters = typing.TypedDict('MakeAverageVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["make_average_volume"],
+    "subjects": list[str],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "out": typing.NotRequired[str | None],
+    "topdir": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[str | None],
+    "sdir": typing.NotRequired[str | None],
+    "force_flag": bool,
+    "keep_all_orig_flag": bool,
+    "no_aseg_flag": bool,
+    "ctab": typing.NotRequired[str | None],
+    "ctab_default_flag": bool,
+    "echo_flag": bool,
+    "nocleanup_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 {
+        "make_average_volume": make_average_volume_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 MakeAverageVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_average_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def make_average_volume_params(
+    subjects: list[str],
+    fsgd: InputPathType | None = None,
+    out: str | None = None,
+    topdir: str | None = None,
+    xform: str | None = None,
+    sdir: str | None = None,
+    force_flag: bool = False,
+    keep_all_orig_flag: bool = False,
+    no_aseg_flag: bool = False,
+    ctab: str | None = None,
+    ctab_default_flag: bool = False,
+    echo_flag: bool = False,
+    nocleanup_flag: bool = False,
+) -> MakeAverageVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects: List of subjects to include in the average.
+        fsgd: File containing subject list for averaging.
+        out: Output average subject name. Default is 'average'.
+        topdir: Directory to put data and link to SUBJECTS_DIR.
+        xform: Transformation name to use, default is talairach.xfm.
+        sdir: Use specified SUBJECTS_DIR instead of the environment's one.
+        force_flag: Overwrite existing average subject data.
+        keep_all_orig_flag: Concatenate all original volumes into\
+            mri/orig.all.mgz.
+        no_aseg_flag: Do not create 'average' aseg.
+        ctab: Embed colortable into segmentations.
+        ctab_default_flag: Embed FreeSurferColorLUT.txt into segmentations.
+        echo_flag: Enable command echo for debugging.
+        nocleanup_flag: Do not delete temporary files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_average_volume",
+        "subjects": subjects,
+        "force_flag": force_flag,
+        "keep_all_orig_flag": keep_all_orig_flag,
+        "no_aseg_flag": no_aseg_flag,
+        "ctab_default_flag": ctab_default_flag,
+        "echo_flag": echo_flag,
+        "nocleanup_flag": nocleanup_flag,
+    }
+    if fsgd is not None:
+        params["fsgd"] = fsgd
+    if out is not None:
+        params["out"] = out
+    if topdir is not None:
+        params["topdir"] = topdir
+    if xform is not None:
+        params["xform"] = xform
+    if sdir is not None:
+        params["sdir"] = sdir
+    if ctab is not None:
+        params["ctab"] = ctab
+    return params
+
+
+def make_average_volume_cargs(
+    params: MakeAverageVolumeParameters,
+    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("make_average_volume")
+    cargs.extend([
+        "--subjects",
+        *params.get("subjects")
+    ])
+    if params.get("fsgd") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("fsgd"))
+        ])
+    if params.get("out") is not None:
+        cargs.extend([
+            "--out",
+            params.get("out")
+        ])
+    if params.get("topdir") is not None:
+        cargs.extend([
+            "--topdir",
+            params.get("topdir")
+        ])
+    if params.get("xform") is not None:
+        cargs.extend([
+            "--xform",
+            params.get("xform")
+        ])
+    if params.get("sdir") is not None:
+        cargs.extend([
+            "--sdir",
+            params.get("sdir")
+        ])
+    if params.get("force_flag"):
+        cargs.append("--force")
+    if params.get("keep_all_orig_flag"):
+        cargs.append("--keep-all-orig")
+    if params.get("no_aseg_flag"):
+        cargs.append("--no-aseg")
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "--ctab",
+            params.get("ctab")
+        ])
+    if params.get("ctab_default_flag"):
+        cargs.append("--ctab-default")
+    if params.get("echo_flag"):
+        cargs.append("--echo")
+    if params.get("nocleanup_flag"):
+        cargs.append("--nocleanup")
+    return cargs
+
+
+def make_average_volume_outputs(
+    params: MakeAverageVolumeParameters,
+    execution: Execution,
+) -> MakeAverageVolumeOutputs:
+    """
+    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 = MakeAverageVolumeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def make_average_volume_execute(
+    params: MakeAverageVolumeParameters,
+    execution: Execution,
+) -> MakeAverageVolumeOutputs:
+    """
+    Creates average volumes from a set of subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeAverageVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_average_volume_cargs(params, execution)
+    ret = make_average_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_average_volume(
+    subjects: list[str],
+    fsgd: InputPathType | None = None,
+    out: str | None = None,
+    topdir: str | None = None,
+    xform: str | None = None,
+    sdir: str | None = None,
+    force_flag: bool = False,
+    keep_all_orig_flag: bool = False,
+    no_aseg_flag: bool = False,
+    ctab: str | None = None,
+    ctab_default_flag: bool = False,
+    echo_flag: bool = False,
+    nocleanup_flag: bool = False,
+    runner: Runner | None = None,
+) -> MakeAverageVolumeOutputs:
+    """
+    Creates average volumes from a set of subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects: List of subjects to include in the average.
+        fsgd: File containing subject list for averaging.
+        out: Output average subject name. Default is 'average'.
+        topdir: Directory to put data and link to SUBJECTS_DIR.
+        xform: Transformation name to use, default is talairach.xfm.
+        sdir: Use specified SUBJECTS_DIR instead of the environment's one.
+        force_flag: Overwrite existing average subject data.
+        keep_all_orig_flag: Concatenate all original volumes into\
+            mri/orig.all.mgz.
+        no_aseg_flag: Do not create 'average' aseg.
+        ctab: Embed colortable into segmentations.
+        ctab_default_flag: Embed FreeSurferColorLUT.txt into segmentations.
+        echo_flag: Enable command echo for debugging.
+        nocleanup_flag: Do not delete temporary files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeAverageVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_AVERAGE_VOLUME_METADATA)
+    params = make_average_volume_params(
+        subjects=subjects,
+        fsgd=fsgd,
+        out=out,
+        topdir=topdir,
+        xform=xform,
+        sdir=sdir,
+        force_flag=force_flag,
+        keep_all_orig_flag=keep_all_orig_flag,
+        no_aseg_flag=no_aseg_flag,
+        ctab=ctab,
+        ctab_default_flag=ctab_default_flag,
+        echo_flag=echo_flag,
+        nocleanup_flag=nocleanup_flag,
+    )
+    return make_average_volume_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_AVERAGE_VOLUME_METADATA",
+    "MakeAverageVolumeOutputs",
+    "MakeAverageVolumeParameters",
+    "make_average_volume",
+    "make_average_volume_params",
+]