niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwi2mask.py

@@ -0,0 +1,570 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWI2MASK_METADATA = Metadata(
+    id="5345247ad41518ec6a872de4d754e7c58b01dff1.boutiques",
+    name="dwi2mask",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Dwi2maskFslgradParamsDictNoTag = typing.TypedDict('_Dwi2maskFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2maskFslgradParamsDictTagged = typing.TypedDict('Dwi2maskFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2maskFslgradParamsDict = _Dwi2maskFslgradParamsDictNoTag | Dwi2maskFslgradParamsDictTagged
+
+
+_Dwi2maskConfigParamsDictNoTag = typing.TypedDict('_Dwi2maskConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Dwi2maskConfigParamsDictTagged = typing.TypedDict('Dwi2maskConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Dwi2maskConfigParamsDict = _Dwi2maskConfigParamsDictNoTag | Dwi2maskConfigParamsDictTagged
+
+
+_Dwi2maskParamsDictNoTag = typing.TypedDict('_Dwi2maskParamsDictNoTag', {
+    "clean_scale": typing.NotRequired[int | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2maskFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2maskConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Dwi2maskParamsDictTagged = typing.TypedDict('Dwi2maskParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dwi2mask"],
+    "clean_scale": typing.NotRequired[int | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2maskFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2maskConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Dwi2maskParamsDict = _Dwi2maskParamsDictNoTag | Dwi2maskParamsDictTagged
+
+
+def dwi2mask_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Dwi2maskFslgradParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def dwi2mask_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2maskFslgradParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("bvecs", None) is None:
+        raise StyxValidationError("`bvecs` must not be None")
+    if not isinstance(params["bvecs"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvecs` has the wrong type: Received `{type(params.get("bvecs", None))}` expected `InputPathType`')
+    if params.get("bvals", None) is None:
+        raise StyxValidationError("`bvals` must not be None")
+    if not isinstance(params["bvals"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvals` has the wrong type: Received `{type(params.get("bvals", None))}` expected `InputPathType`')
+
+
+def dwi2mask_fslgrad_cargs(
+    params: Dwi2maskFslgradParamsDict,
+    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("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
+    return cargs
+
+
+def dwi2mask_config(
+    key: str,
+    value: str,
+) -> Dwi2maskConfigParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def dwi2mask_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2maskConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def dwi2mask_config_cargs(
+    params: Dwi2maskConfigParamsDict,
+    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("-config")
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class Dwi2maskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Dwi2maskParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output whole-brain mask image"""
+
+
+def dwi2mask_params(
+    input_: InputPathType,
+    output: str,
+    clean_scale: int | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2maskFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2maskConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Dwi2maskParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input DWI image containing volumes that are both diffusion\
+            weighted and b=0.
+        output: the output whole-brain mask image.
+        clean_scale: the maximum scale used to cut bridges. A certain maximum\
+            scale cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            Setting this to 0 disables the mask cleaning step. (Default: 2).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "mrtrix/dwi2mask",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if clean_scale is not None:
+        params["clean_scale"] = clean_scale
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dwi2mask_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2maskParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("clean_scale", None) is not None:
+        if not isinstance(params["clean_scale"], int):
+            raise StyxValidationError(f'`clean_scale` has the wrong type: Received `{type(params.get("clean_scale", None))}` expected `int | None`')
+    if params.get("grad", None) is not None:
+        if not isinstance(params["grad"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
+    if params.get("fslgrad", None) is not None:
+        dwi2mask_fslgrad_validate(params["fslgrad"])
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[Dwi2maskConfigParamsDict] | None`')
+        for e in params["config"]:
+            dwi2mask_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def dwi2mask_cargs(
+    params: Dwi2maskParamsDict,
+    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("dwi2mask")
+    if params.get("clean_scale", None) is not None:
+        cargs.extend([
+            "-clean_scale",
+            str(params.get("clean_scale", None))
+        ])
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(dwi2mask_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [dwi2mask_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def dwi2mask_outputs(
+    params: Dwi2maskParamsDict,
+    execution: Execution,
+) -> Dwi2maskOutputs:
+    """
+    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 = Dwi2maskOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def dwi2mask_execute(
+    params: Dwi2maskParamsDict,
+    runner: Runner | None = None,
+) -> Dwi2maskOutputs:
+    """
+    dwi2mask
+    
+    Generates a whole brain mask from a DWI image.
+    
+    All diffusion weighted and b=0 volumes are used to obtain a mask that
+    includes both brain tissue and CSF.
+    
+    In a second step peninsula-like extensions, where the peninsula itself is
+    wider than the bridge connecting it to the mask, are removed. This may help
+    removing artefacts and non-brain parts, e.g. eyes, from the mask.
+    
+    References:
+    
+    Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function
+    estimation from single-shell or multi-shell diffusion MR data without a
+    co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion
+    MRI, 2016, 5.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2maskOutputs`).
+    """
+    dwi2mask_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWI2MASK_METADATA)
+    params = execution.params(params)
+    cargs = dwi2mask_cargs(params, execution)
+    ret = dwi2mask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwi2mask(
+    input_: InputPathType,
+    output: str,
+    clean_scale: int | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2maskFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2maskConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Dwi2maskOutputs:
+    """
+    dwi2mask
+    
+    Generates a whole brain mask from a DWI image.
+    
+    All diffusion weighted and b=0 volumes are used to obtain a mask that
+    includes both brain tissue and CSF.
+    
+    In a second step peninsula-like extensions, where the peninsula itself is
+    wider than the bridge connecting it to the mask, are removed. This may help
+    removing artefacts and non-brain parts, e.g. eyes, from the mask.
+    
+    References:
+    
+    Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function
+    estimation from single-shell or multi-shell diffusion MR data without a
+    co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion
+    MRI, 2016, 5.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input DWI image containing volumes that are both diffusion\
+            weighted and b=0.
+        output: the output whole-brain mask image.
+        clean_scale: the maximum scale used to cut bridges. A certain maximum\
+            scale cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            Setting this to 0 disables the mask cleaning step. (Default: 2).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2maskOutputs`).
+    """
+    params = dwi2mask_params(
+        clean_scale=clean_scale,
+        grad=grad,
+        fslgrad=fslgrad,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return dwi2mask_execute(params, runner)
+
+
+__all__ = [
+    "DWI2MASK_METADATA",
+    "Dwi2maskConfigParamsDict",
+    "Dwi2maskConfigParamsDictTagged",
+    "Dwi2maskFslgradParamsDict",
+    "Dwi2maskFslgradParamsDictTagged",
+    "Dwi2maskOutputs",
+    "Dwi2maskParamsDict",
+    "Dwi2maskParamsDictTagged",
+    "dwi2mask",
+    "dwi2mask_config",
+    "dwi2mask_execute",
+    "dwi2mask_fslgrad",
+    "dwi2mask_params",
+]