niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/lpcregister.py

@@ -0,0 +1,326 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+LPCREGISTER_METADATA = Metadata(
+    id="e5a5971735d364dfe8f37cf7d53f26828a5b15b4.boutiques",
+    name="lpcregister",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+LpcregisterParameters = typing.TypedDict('LpcregisterParameters', {
+    "__STYX_TYPE__": typing.Literal["lpcregister"],
+    "subject_id": str,
+    "mov_volume": str,
+    "reg_file": str,
+    "dof_9": bool,
+    "dof_12": bool,
+    "frame_number": typing.NotRequired[float | None],
+    "mid_frame": bool,
+    "fsvol": typing.NotRequired[str | None],
+    "output_volume": typing.NotRequired[str | None],
+    "tmp_dir": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "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 {
+        "lpcregister": lpcregister_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 {
+        "lpcregister": lpcregister_outputs,
+    }.get(t)
+
+
+class LpcregisterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `lpcregister(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_reg_file: OutputPathType
+    """Output registration file in FreeSurfer format."""
+    resampled_volume: OutputPathType | None
+    """The resampled movable volume if --o is specified."""
+
+
+def lpcregister_params(
+    subject_id: str,
+    mov_volume: str,
+    reg_file: str,
+    dof_9: bool = False,
+    dof_12: bool = False,
+    frame_number: float | None = None,
+    mid_frame: bool = False,
+    fsvol: str | None = None,
+    output_volume: str | None = None,
+    tmp_dir: str | None = None,
+    no_cleanup: bool = False,
+    version: bool = False,
+    help_: bool = False,
+) -> LpcregisterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Subject ID found in SUBJECTS_DIR. The reference volume is\
+            the mri/brain volume (modifiable with --fsvol). Converted to analyze\
+            using mri_convert.
+        mov_volume: Volume identifier of the movable volume. Must be specified\
+            suitably for mri_convert. Uses first frame unless --frame is specified.
+        reg_file: Output registration file mapping RAS in the reference to RAS\
+            in the movable. The file/matrix format is understood by freesurfer.
+        dof_9: Use 9 degrees of freedom; default is 6.
+        dof_12: Use 12 degrees of freedom; default is 6.
+        frame_number: Specify the frame number other than the first. For SPM\
+            analyze, specify the file corresponding to the desired frame as each\
+            file only has one frame.
+        mid_frame: Register to the middle frame of the mov volume as the\
+            template. Cannot be used with --frame.
+        fsvol: Use FreeSurfer volume id; default is brainmask.
+        output_volume: Output volume file for resampled mov.
+        tmp_dir: Specify temporary directory (implies --nocleanup).
+        no_cleanup: Do not delete temporary files.
+        version: Print the version and exit.
+        help_: Print help information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "lpcregister",
+        "subject_id": subject_id,
+        "mov_volume": mov_volume,
+        "reg_file": reg_file,
+        "dof_9": dof_9,
+        "dof_12": dof_12,
+        "mid_frame": mid_frame,
+        "no_cleanup": no_cleanup,
+        "version": version,
+        "help": help_,
+    }
+    if frame_number is not None:
+        params["frame_number"] = frame_number
+    if fsvol is not None:
+        params["fsvol"] = fsvol
+    if output_volume is not None:
+        params["output_volume"] = output_volume
+    if tmp_dir is not None:
+        params["tmp_dir"] = tmp_dir
+    return params
+
+
+def lpcregister_cargs(
+    params: LpcregisterParameters,
+    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("lpcregister")
+    cargs.extend([
+        "--s",
+        params.get("subject_id")
+    ])
+    cargs.extend([
+        "--mov",
+        params.get("mov_volume")
+    ])
+    cargs.extend([
+        "--reg",
+        params.get("reg_file")
+    ])
+    if params.get("dof_9"):
+        cargs.append("--9")
+    if params.get("dof_12"):
+        cargs.append("--12")
+    if params.get("frame_number") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame_number"))
+        ])
+    if params.get("mid_frame"):
+        cargs.append("--mid-frame")
+    if params.get("fsvol") is not None:
+        cargs.extend([
+            "--fsvol",
+            params.get("fsvol")
+        ])
+    if params.get("output_volume") is not None:
+        cargs.extend([
+            "--o",
+            params.get("output_volume")
+        ])
+    if params.get("tmp_dir") is not None:
+        cargs.extend([
+            "--tmp",
+            params.get("tmp_dir")
+        ])
+    if params.get("no_cleanup"):
+        cargs.append("--nocleanup")
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("help"):
+        cargs.append("--help")
+    return cargs
+
+
+def lpcregister_outputs(
+    params: LpcregisterParameters,
+    execution: Execution,
+) -> LpcregisterOutputs:
+    """
+    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 = LpcregisterOutputs(
+        root=execution.output_file("."),
+        output_reg_file=execution.output_file("register.dat"),
+        resampled_volume=execution.output_file(params.get("output_volume")) if (params.get("output_volume") is not None) else None,
+    )
+    return ret
+
+
+def lpcregister_execute(
+    params: LpcregisterParameters,
+    execution: Execution,
+) -> LpcregisterOutputs:
+    """
+    Registers a volume to its FreeSurfer anatomical using Local Pearson Correlation
+    (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer register.dat file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `LpcregisterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = lpcregister_cargs(params, execution)
+    ret = lpcregister_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def lpcregister(
+    subject_id: str,
+    mov_volume: str,
+    reg_file: str,
+    dof_9: bool = False,
+    dof_12: bool = False,
+    frame_number: float | None = None,
+    mid_frame: bool = False,
+    fsvol: str | None = None,
+    output_volume: str | None = None,
+    tmp_dir: str | None = None,
+    no_cleanup: bool = False,
+    version: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> LpcregisterOutputs:
+    """
+    Registers a volume to its FreeSurfer anatomical using Local Pearson Correlation
+    (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer register.dat file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_id: Subject ID found in SUBJECTS_DIR. The reference volume is\
+            the mri/brain volume (modifiable with --fsvol). Converted to analyze\
+            using mri_convert.
+        mov_volume: Volume identifier of the movable volume. Must be specified\
+            suitably for mri_convert. Uses first frame unless --frame is specified.
+        reg_file: Output registration file mapping RAS in the reference to RAS\
+            in the movable. The file/matrix format is understood by freesurfer.
+        dof_9: Use 9 degrees of freedom; default is 6.
+        dof_12: Use 12 degrees of freedom; default is 6.
+        frame_number: Specify the frame number other than the first. For SPM\
+            analyze, specify the file corresponding to the desired frame as each\
+            file only has one frame.
+        mid_frame: Register to the middle frame of the mov volume as the\
+            template. Cannot be used with --frame.
+        fsvol: Use FreeSurfer volume id; default is brainmask.
+        output_volume: Output volume file for resampled mov.
+        tmp_dir: Specify temporary directory (implies --nocleanup).
+        no_cleanup: Do not delete temporary files.
+        version: Print the version and exit.
+        help_: Print help information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `LpcregisterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LPCREGISTER_METADATA)
+    params = lpcregister_params(
+        subject_id=subject_id,
+        mov_volume=mov_volume,
+        reg_file=reg_file,
+        dof_9=dof_9,
+        dof_12=dof_12,
+        frame_number=frame_number,
+        mid_frame=mid_frame,
+        fsvol=fsvol,
+        output_volume=output_volume,
+        tmp_dir=tmp_dir,
+        no_cleanup=no_cleanup,
+        version=version,
+        help_=help_,
+    )
+    return lpcregister_execute(params, execution)
+
+
+__all__ = [
+    "LPCREGISTER_METADATA",
+    "LpcregisterOutputs",
+    "LpcregisterParameters",
+    "lpcregister",
+    "lpcregister_params",
+]

niwrap_freesurfer/freesurfer/lta_convert.py

@@ -0,0 +1,273 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+LTA_CONVERT_METADATA = Metadata(
+    id="daaa6767af53c23e0e3f62c31924d12dbc6e0eaa.boutiques",
+    name="lta_convert",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+LtaConvertParameters = typing.TypedDict('LtaConvertParameters', {
+    "__STYX_TYPE__": typing.Literal["lta_convert"],
+    "in_vox": typing.NotRequired[InputPathType | None],
+    "out_vox": typing.NotRequired[str | None],
+    "invert": bool,
+    "ltavox2vox": bool,
+    "ltatkreg": bool,
+    "src_geometry": typing.NotRequired[InputPathType | None],
+    "trg_geometry": typing.NotRequired[InputPathType | None],
+    "trg_conform": bool,
+    "subject_name": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "lta_convert": lta_convert_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 {
+        "lta_convert": lta_convert_outputs,
+    }.get(t)
+
+
+class LtaConvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `lta_convert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_transform_file: OutputPathType | None
+    """Output transformed file."""
+
+
+def lta_convert_params(
+    in_vox: InputPathType | None = None,
+    out_vox: str | None = None,
+    invert: bool = False,
+    ltavox2vox: bool = False,
+    ltatkreg: bool = False,
+    src_geometry: InputPathType | None = None,
+    trg_geometry: InputPathType | None = None,
+    trg_conform: bool = False,
+    subject_name: str | None = None,
+) -> LtaConvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_vox: Input transform in source image space (inverse VOX2VOX).
+        out_vox: Output transform in source image space (inverse VOX2VOX).
+        invert: Inverts transform.
+        ltavox2vox: Output type VOX2VOX (default RAS2RAS) with --ltaout.
+        ltatkreg: Output type REGISTER_DAT (default RAS2RAS) with --ltaout.
+        src_geometry: Specify src image geometry (mov volume for\
+            TKREG/register.dat).
+        trg_geometry: Specify trg image geometry.
+        trg_conform: Conform trg image geometry (COR standard).
+        subject_name: Specify subject name (overrides if input has subject name\
+            defined).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "lta_convert",
+        "invert": invert,
+        "ltavox2vox": ltavox2vox,
+        "ltatkreg": ltatkreg,
+        "trg_conform": trg_conform,
+    }
+    if in_vox is not None:
+        params["in_vox"] = in_vox
+    if out_vox is not None:
+        params["out_vox"] = out_vox
+    if src_geometry is not None:
+        params["src_geometry"] = src_geometry
+    if trg_geometry is not None:
+        params["trg_geometry"] = trg_geometry
+    if subject_name is not None:
+        params["subject_name"] = subject_name
+    return params
+
+
+def lta_convert_cargs(
+    params: LtaConvertParameters,
+    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("lta_convert")
+    if params.get("in_vox") is not None:
+        cargs.extend([
+            "--invox",
+            execution.input_file(params.get("in_vox"))
+        ])
+    if params.get("out_vox") is not None:
+        cargs.extend([
+            "--outvox",
+            params.get("out_vox")
+        ])
+    if params.get("invert"):
+        cargs.append("--invert")
+    if params.get("ltavox2vox"):
+        cargs.append("--ltavox2vox")
+    if params.get("ltatkreg"):
+        cargs.append("--ltatkreg")
+    if params.get("src_geometry") is not None:
+        cargs.extend([
+            "--src",
+            execution.input_file(params.get("src_geometry"))
+        ])
+    if params.get("trg_geometry") is not None:
+        cargs.extend([
+            "--trg",
+            execution.input_file(params.get("trg_geometry"))
+        ])
+    if params.get("trg_conform"):
+        cargs.append("--trgconform")
+    if params.get("subject_name") is not None:
+        cargs.extend([
+            "--subject",
+            params.get("subject_name")
+        ])
+    return cargs
+
+
+def lta_convert_outputs(
+    params: LtaConvertParameters,
+    execution: Execution,
+) -> LtaConvertOutputs:
+    """
+    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 = LtaConvertOutputs(
+        root=execution.output_file("."),
+        output_transform_file=execution.output_file(params.get("out_vox")) if (params.get("out_vox") is not None) else None,
+    )
+    return ret
+
+
+def lta_convert_execute(
+    params: LtaConvertParameters,
+    execution: Execution,
+) -> LtaConvertOutputs:
+    """
+    This program converts between different linear transform formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `LtaConvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = lta_convert_cargs(params, execution)
+    ret = lta_convert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def lta_convert(
+    in_vox: InputPathType | None = None,
+    out_vox: str | None = None,
+    invert: bool = False,
+    ltavox2vox: bool = False,
+    ltatkreg: bool = False,
+    src_geometry: InputPathType | None = None,
+    trg_geometry: InputPathType | None = None,
+    trg_conform: bool = False,
+    subject_name: str | None = None,
+    runner: Runner | None = None,
+) -> LtaConvertOutputs:
+    """
+    This program converts between different linear transform formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        in_vox: Input transform in source image space (inverse VOX2VOX).
+        out_vox: Output transform in source image space (inverse VOX2VOX).
+        invert: Inverts transform.
+        ltavox2vox: Output type VOX2VOX (default RAS2RAS) with --ltaout.
+        ltatkreg: Output type REGISTER_DAT (default RAS2RAS) with --ltaout.
+        src_geometry: Specify src image geometry (mov volume for\
+            TKREG/register.dat).
+        trg_geometry: Specify trg image geometry.
+        trg_conform: Conform trg image geometry (COR standard).
+        subject_name: Specify subject name (overrides if input has subject name\
+            defined).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `LtaConvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LTA_CONVERT_METADATA)
+    params = lta_convert_params(
+        in_vox=in_vox,
+        out_vox=out_vox,
+        invert=invert,
+        ltavox2vox=ltavox2vox,
+        ltatkreg=ltatkreg,
+        src_geometry=src_geometry,
+        trg_geometry=trg_geometry,
+        trg_conform=trg_conform,
+        subject_name=subject_name,
+    )
+    return lta_convert_execute(params, execution)
+
+
+__all__ = [
+    "LTA_CONVERT_METADATA",
+    "LtaConvertOutputs",
+    "LtaConvertParameters",
+    "lta_convert",
+    "lta_convert_params",
+]