niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/make_segvol_table.py

@@ -0,0 +1,295 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_SEGVOL_TABLE_METADATA = Metadata(
+    id="584e18cf5964aa90ad96025eab578f07dcec865b.boutiques",
+    name="make-segvol-table",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MakeSegvolTableParameters = typing.TypedDict('MakeSegvolTableParameters', {
+    "__STYX_TYPE__": typing.Literal["make-segvol-table"],
+    "subjects": list[str],
+    "subject_file": InputPathType,
+    "outfile": str,
+    "idmap": typing.NotRequired[InputPathType | None],
+    "structure_ids": typing.NotRequired[list[str] | None],
+    "segdir": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "version": bool,
+    "help": 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-segvol-table": make_segvol_table_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 {
+        "make-segvol-table": make_segvol_table_outputs,
+    }.get(t)
+
+
+class MakeSegvolTableOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_segvol_table(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_table: OutputPathType
+    """Output text file containing the table of subcortical structure
+    volumes."""
+
+
+def make_segvol_table_params(
+    subjects: list[str],
+    subject_file: InputPathType,
+    outfile: str,
+    idmap: InputPathType | None = None,
+    structure_ids: list[str] | None = None,
+    segdir: str | None = None,
+    subjects_dir: str | None = None,
+    umask: str | None = None,
+    version: bool = False,
+    help_: bool = False,
+) -> MakeSegvolTableParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects: List of subject IDs. Each subject should be specified with a\
+            separate -s flag.
+        subject_file: Path to a file containing a list of subjects.
+        outfile: Output file where the table will be saved.
+        idmap: File with structure name and id number. Default is\
+            FREESURFER_HOME/tkmeditColorsCMA.
+        structure_ids: Names of structures to include in the table. Defaults to\
+            all structures.
+        segdir: Segmentation subdirectory name. Default is 'aseg'.
+        subjects_dir: Path to the subjects directory. Default is SUBJECTS_DIR\
+            environment variable.
+        umask: Set UNIX file permission mask.
+        version: Print version and exit.
+        help_: Display help information.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make-segvol-table",
+        "subjects": subjects,
+        "subject_file": subject_file,
+        "outfile": outfile,
+        "version": version,
+        "help": help_,
+    }
+    if idmap is not None:
+        params["idmap"] = idmap
+    if structure_ids is not None:
+        params["structure_ids"] = structure_ids
+    if segdir is not None:
+        params["segdir"] = segdir
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if umask is not None:
+        params["umask"] = umask
+    return params
+
+
+def make_segvol_table_cargs(
+    params: MakeSegvolTableParameters,
+    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-segvol-table")
+    cargs.extend([
+        "-s",
+        *params.get("subjects")
+    ])
+    cargs.extend([
+        "-sf",
+        execution.input_file(params.get("subject_file"))
+    ])
+    cargs.extend([
+        "-o",
+        params.get("outfile")
+    ])
+    if params.get("idmap") is not None:
+        cargs.extend([
+            "-idmap",
+            execution.input_file(params.get("idmap"))
+        ])
+    if params.get("structure_ids") is not None:
+        cargs.extend([
+            "-id",
+            *params.get("structure_ids")
+        ])
+    if params.get("segdir") is not None:
+        cargs.extend([
+            "-segdir",
+            params.get("segdir")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def make_segvol_table_outputs(
+    params: MakeSegvolTableParameters,
+    execution: Execution,
+) -> MakeSegvolTableOutputs:
+    """
+    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 = MakeSegvolTableOutputs(
+        root=execution.output_file("."),
+        output_table=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def make_segvol_table_execute(
+    params: MakeSegvolTableParameters,
+    execution: Execution,
+) -> MakeSegvolTableOutputs:
+    """
+    Creates a table of volumes of subcortical structures for a given list of
+    subjects using FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeSegvolTableOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_segvol_table_cargs(params, execution)
+    ret = make_segvol_table_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_segvol_table(
+    subjects: list[str],
+    subject_file: InputPathType,
+    outfile: str,
+    idmap: InputPathType | None = None,
+    structure_ids: list[str] | None = None,
+    segdir: str | None = None,
+    subjects_dir: str | None = None,
+    umask: str | None = None,
+    version: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MakeSegvolTableOutputs:
+    """
+    Creates a table of volumes of subcortical structures for a given list of
+    subjects using FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects: List of subject IDs. Each subject should be specified with a\
+            separate -s flag.
+        subject_file: Path to a file containing a list of subjects.
+        outfile: Output file where the table will be saved.
+        idmap: File with structure name and id number. Default is\
+            FREESURFER_HOME/tkmeditColorsCMA.
+        structure_ids: Names of structures to include in the table. Defaults to\
+            all structures.
+        segdir: Segmentation subdirectory name. Default is 'aseg'.
+        subjects_dir: Path to the subjects directory. Default is SUBJECTS_DIR\
+            environment variable.
+        umask: Set UNIX file permission mask.
+        version: Print version and exit.
+        help_: Display help information.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeSegvolTableOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_SEGVOL_TABLE_METADATA)
+    params = make_segvol_table_params(
+        subjects=subjects,
+        subject_file=subject_file,
+        outfile=outfile,
+        idmap=idmap,
+        structure_ids=structure_ids,
+        segdir=segdir,
+        subjects_dir=subjects_dir,
+        umask=umask,
+        version=version,
+        help_=help_,
+    )
+    return make_segvol_table_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_SEGVOL_TABLE_METADATA",
+    "MakeSegvolTableOutputs",
+    "MakeSegvolTableParameters",
+    "make_segvol_table",
+    "make_segvol_table_params",
+]

niwrap_freesurfer/freesurfer/make_symmetric.py

@@ -0,0 +1,211 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_SYMMETRIC_METADATA = Metadata(
+    id="0edab2e26b68afca9fa6531a0a4823dd6acee05b.boutiques",
+    name="make_symmetric",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MakeSymmetricParameters = typing.TypedDict('MakeSymmetricParameters', {
+    "__STYX_TYPE__": typing.Literal["make_symmetric"],
+    "hemi": str,
+    "input_file": InputPathType,
+    "output_file": str,
+    "transform_map": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "make_symmetric": make_symmetric_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 {
+        "make_symmetric": make_symmetric_outputs,
+    }.get(t)
+
+
+class MakeSymmetricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_symmetric(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    processed_output: OutputPathType
+    """Output image file after processing."""
+    map_output: OutputPathType
+    """Transformation map file mapping the input to the upright space."""
+
+
+def make_symmetric_params(
+    hemi: str,
+    input_file: InputPathType,
+    output_file: str,
+    transform_map: str,
+) -> MakeSymmetricParameters:
+    """
+    Build parameters.
+    
+    Args:
+        hemi: The hemisphere to mirror; accepted values are 'lh' for left\
+            hemisphere or 'rh' for right hemisphere.
+        input_file: Input image in .mgz format.
+        output_file: Output image in .mgz format resulting from the symmetric\
+            processing.
+        transform_map: Transformation map in .lta format mapping the input to\
+            the upright space.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_symmetric",
+        "hemi": hemi,
+        "input_file": input_file,
+        "output_file": output_file,
+        "transform_map": transform_map,
+    }
+    return params
+
+
+def make_symmetric_cargs(
+    params: MakeSymmetricParameters,
+    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_symmetric")
+    cargs.append(params.get("hemi"))
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(params.get("output_file"))
+    cargs.append(params.get("transform_map"))
+    return cargs
+
+
+def make_symmetric_outputs(
+    params: MakeSymmetricParameters,
+    execution: Execution,
+) -> MakeSymmetricOutputs:
+    """
+    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 = MakeSymmetricOutputs(
+        root=execution.output_file("."),
+        processed_output=execution.output_file(params.get("output_file")),
+        map_output=execution.output_file(params.get("transform_map")),
+    )
+    return ret
+
+
+def make_symmetric_execute(
+    params: MakeSymmetricParameters,
+    execution: Execution,
+) -> MakeSymmetricOutputs:
+    """
+    Registers an input image to its left/right reversed version using
+    mri_robust_register in a half-way space and mirrors the selected hemisphere.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeSymmetricOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_symmetric_cargs(params, execution)
+    ret = make_symmetric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_symmetric(
+    hemi: str,
+    input_file: InputPathType,
+    output_file: str,
+    transform_map: str,
+    runner: Runner | None = None,
+) -> MakeSymmetricOutputs:
+    """
+    Registers an input image to its left/right reversed version using
+    mri_robust_register in a half-way space and mirrors the selected hemisphere.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        hemi: The hemisphere to mirror; accepted values are 'lh' for left\
+            hemisphere or 'rh' for right hemisphere.
+        input_file: Input image in .mgz format.
+        output_file: Output image in .mgz format resulting from the symmetric\
+            processing.
+        transform_map: Transformation map in .lta format mapping the input to\
+            the upright space.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeSymmetricOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_SYMMETRIC_METADATA)
+    params = make_symmetric_params(
+        hemi=hemi,
+        input_file=input_file,
+        output_file=output_file,
+        transform_map=transform_map,
+    )
+    return make_symmetric_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_SYMMETRIC_METADATA",
+    "MakeSymmetricOutputs",
+    "MakeSymmetricParameters",
+    "make_symmetric",
+    "make_symmetric_params",
+]

niwrap_freesurfer/freesurfer/make_upright.py

@@ -0,0 +1,196 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAKE_UPRIGHT_METADATA = Metadata(
+    id="f69f1f73df7f80db3bbc666008c56b37f2fb8894.boutiques",
+    name="make_upright",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MakeUprightParameters = typing.TypedDict('MakeUprightParameters', {
+    "__STYX_TYPE__": typing.Literal["make_upright"],
+    "input_image": InputPathType,
+    "output_image": str,
+    "transformation_map": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "make_upright": make_upright_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 {
+        "make_upright": make_upright_outputs,
+    }.get(t)
+
+
+class MakeUprightOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `make_upright(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    registered_image: OutputPathType
+    """Registered upright MRI image"""
+
+
+def make_upright_params(
+    input_image: InputPathType,
+    output_image: str,
+    transformation_map: InputPathType,
+) -> MakeUprightParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input MRI image file in .mgz format.
+        output_image: Output MRI image file in .mgz format.
+        transformation_map: Transformation map file in .lta format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "make_upright",
+        "input_image": input_image,
+        "output_image": output_image,
+        "transformation_map": transformation_map,
+    }
+    return params
+
+
+def make_upright_cargs(
+    params: MakeUprightParameters,
+    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_upright")
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(params.get("output_image"))
+    cargs.append(execution.input_file(params.get("transformation_map")))
+    return cargs
+
+
+def make_upright_outputs(
+    params: MakeUprightParameters,
+    execution: Execution,
+) -> MakeUprightOutputs:
+    """
+    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 = MakeUprightOutputs(
+        root=execution.output_file("."),
+        registered_image=execution.output_file(params.get("output_image")),
+    )
+    return ret
+
+
+def make_upright_execute(
+    params: MakeUprightParameters,
+    execution: Execution,
+) -> MakeUprightOutputs:
+    """
+    Registers MRI input to the left/right reversed version using mri_robust_register
+    and making use of the half-way space, resulting in an upright, forward facing
+    head position.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MakeUprightOutputs`).
+    """
+    params = execution.params(params)
+    cargs = make_upright_cargs(params, execution)
+    ret = make_upright_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def make_upright(
+    input_image: InputPathType,
+    output_image: str,
+    transformation_map: InputPathType,
+    runner: Runner | None = None,
+) -> MakeUprightOutputs:
+    """
+    Registers MRI input to the left/right reversed version using mri_robust_register
+    and making use of the half-way space, resulting in an upright, forward facing
+    head position.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: Input MRI image file in .mgz format.
+        output_image: Output MRI image file in .mgz format.
+        transformation_map: Transformation map file in .lta format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MakeUprightOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_UPRIGHT_METADATA)
+    params = make_upright_params(
+        input_image=input_image,
+        output_image=output_image,
+        transformation_map=transformation_map,
+    )
+    return make_upright_execute(params, execution)
+
+
+__all__ = [
+    "MAKE_UPRIGHT_METADATA",
+    "MakeUprightOutputs",
+    "MakeUprightParameters",
+    "make_upright",
+    "make_upright_params",
+]