niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwiextract.py

@@ -0,0 +1,1111 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWIEXTRACT_METADATA = Metadata(
+    id="0021ca6ba5d653dd2d95adc256257bec0ea68206.boutiques",
+    name="dwiextract",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_DwiextractFslgradParamsDictNoTag = typing.TypedDict('_DwiextractFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+DwiextractFslgradParamsDictTagged = typing.TypedDict('DwiextractFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+DwiextractFslgradParamsDict = _DwiextractFslgradParamsDictNoTag | DwiextractFslgradParamsDictTagged
+
+
+_DwiextractExportGradFslParamsDictNoTag = typing.TypedDict('_DwiextractExportGradFslParamsDictNoTag', {
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+DwiextractExportGradFslParamsDictTagged = typing.TypedDict('DwiextractExportGradFslParamsDictTagged', {
+    "@type": typing.Literal["export_grad_fsl"],
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+DwiextractExportGradFslParamsDict = _DwiextractExportGradFslParamsDictNoTag | DwiextractExportGradFslParamsDictTagged
+
+
+_DwiextractImportPeEddyParamsDictNoTag = typing.TypedDict('_DwiextractImportPeEddyParamsDictNoTag', {
+    "config": InputPathType,
+    "indices": InputPathType,
+})
+DwiextractImportPeEddyParamsDictTagged = typing.TypedDict('DwiextractImportPeEddyParamsDictTagged', {
+    "@type": typing.Literal["import_pe_eddy"],
+    "config": InputPathType,
+    "indices": InputPathType,
+})
+DwiextractImportPeEddyParamsDict = _DwiextractImportPeEddyParamsDictNoTag | DwiextractImportPeEddyParamsDictTagged
+
+
+_DwiextractVariousStringParamsDictNoTag = typing.TypedDict('_DwiextractVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+DwiextractVariousStringParamsDictTagged = typing.TypedDict('DwiextractVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+DwiextractVariousStringParamsDict = _DwiextractVariousStringParamsDictNoTag | DwiextractVariousStringParamsDictTagged
+
+
+_DwiextractVariousFileParamsDictNoTag = typing.TypedDict('_DwiextractVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+DwiextractVariousFileParamsDictTagged = typing.TypedDict('DwiextractVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+DwiextractVariousFileParamsDict = _DwiextractVariousFileParamsDictNoTag | DwiextractVariousFileParamsDictTagged
+
+
+_DwiextractConfigParamsDictNoTag = typing.TypedDict('_DwiextractConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+DwiextractConfigParamsDictTagged = typing.TypedDict('DwiextractConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+DwiextractConfigParamsDict = _DwiextractConfigParamsDictNoTag | DwiextractConfigParamsDictTagged
+
+
+_DwiextractParamsDictNoTag = typing.TypedDict('_DwiextractParamsDictNoTag', {
+    "bzero": bool,
+    "no_bzero": bool,
+    "singleshell": bool,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DwiextractFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[DwiextractExportGradFslParamsDict | None],
+    "import_pe_table": typing.NotRequired[InputPathType | None],
+    "import_pe_eddy": typing.NotRequired[DwiextractImportPeEddyParamsDict | None],
+    "pe": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[DwiextractVariousStringParamsDictTagged, DwiextractVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DwiextractConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+DwiextractParamsDictTagged = typing.TypedDict('DwiextractParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dwiextract"],
+    "bzero": bool,
+    "no_bzero": bool,
+    "singleshell": bool,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DwiextractFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[DwiextractExportGradFslParamsDict | None],
+    "import_pe_table": typing.NotRequired[InputPathType | None],
+    "import_pe_eddy": typing.NotRequired[DwiextractImportPeEddyParamsDict | None],
+    "pe": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[DwiextractVariousStringParamsDictTagged, DwiextractVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DwiextractConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+DwiextractParamsDict = _DwiextractParamsDictNoTag | DwiextractParamsDictTagged
+
+
+def dwiextract_strides_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": dwiextract_various_string_cargs,
+        "VariousFile": dwiextract_various_file_cargs,
+    }.get(t)
+
+
+def dwiextract_strides_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": dwiextract_various_string_validate,
+        "VariousFile": dwiextract_various_file_validate,
+    }.get(t)
+
+
+def dwiextract_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> DwiextractFslgradParamsDictTagged:
+    """
+    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 dwiextract_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractFslgradParamsDict` 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 dwiextract_fslgrad_cargs(
+    params: DwiextractFslgradParamsDict,
+    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
+
+
+class DwiextractExportGradFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DwiextractExportGradFslParamsDict | None(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    bvecs_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+    bvals_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+
+
+def dwiextract_export_grad_fsl(
+    bvecs_path: str,
+    bvals_path: str,
+) -> DwiextractExportGradFslParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+        bvals_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "export_grad_fsl",
+        "bvecs_path": bvecs_path,
+        "bvals_path": bvals_path,
+    }
+    return params
+
+
+def dwiextract_export_grad_fsl_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractExportGradFslParamsDict` 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_path", None) is None:
+        raise StyxValidationError("`bvecs_path` must not be None")
+    if not isinstance(params["bvecs_path"], str):
+        raise StyxValidationError(f'`bvecs_path` has the wrong type: Received `{type(params.get("bvecs_path", None))}` expected `str`')
+    if params.get("bvals_path", None) is None:
+        raise StyxValidationError("`bvals_path` must not be None")
+    if not isinstance(params["bvals_path"], str):
+        raise StyxValidationError(f'`bvals_path` has the wrong type: Received `{type(params.get("bvals_path", None))}` expected `str`')
+
+
+def dwiextract_export_grad_fsl_cargs(
+    params: DwiextractExportGradFslParamsDict,
+    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("-export_grad_fsl")
+    cargs.append(params.get("bvecs_path", None))
+    cargs.append(params.get("bvals_path", None))
+    return cargs
+
+
+def dwiextract_export_grad_fsl_outputs(
+    params: DwiextractExportGradFslParamsDict,
+    execution: Execution,
+) -> DwiextractExportGradFslOutputs:
+    """
+    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 = DwiextractExportGradFslOutputs(
+        root=execution.output_file("."),
+        bvecs_path=execution.output_file(params.get("bvecs_path", None)),
+        bvals_path=execution.output_file(params.get("bvals_path", None)),
+    )
+    return ret
+
+
+def dwiextract_import_pe_eddy(
+    config: InputPathType,
+    indices: InputPathType,
+) -> DwiextractImportPeEddyParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        config: import phase-encoding information from an EDDY-style config /\
+            index file pair.
+        indices: import phase-encoding information from an EDDY-style config /\
+            index file pair.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "import_pe_eddy",
+        "config": config,
+        "indices": indices,
+    }
+    return params
+
+
+def dwiextract_import_pe_eddy_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractImportPeEddyParamsDict` 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("config", None) is None:
+        raise StyxValidationError("`config` must not be None")
+    if not isinstance(params["config"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `InputPathType`')
+    if params.get("indices", None) is None:
+        raise StyxValidationError("`indices` must not be None")
+    if not isinstance(params["indices"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`indices` has the wrong type: Received `{type(params.get("indices", None))}` expected `InputPathType`')
+
+
+def dwiextract_import_pe_eddy_cargs(
+    params: DwiextractImportPeEddyParamsDict,
+    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("-import_pe_eddy")
+    cargs.append(execution.input_file(params.get("config", None)))
+    cargs.append(execution.input_file(params.get("indices", None)))
+    return cargs
+
+
+def dwiextract_various_string(
+    obj: str,
+) -> DwiextractVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def dwiextract_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractVariousStringParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], str):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `str`')
+
+
+def dwiextract_various_string_cargs(
+    params: DwiextractVariousStringParamsDict,
+    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(params.get("obj", None))
+    return cargs
+
+
+def dwiextract_various_file(
+    obj: InputPathType,
+) -> DwiextractVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def dwiextract_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractVariousFileParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `InputPathType`')
+
+
+def dwiextract_various_file_cargs(
+    params: DwiextractVariousFileParamsDict,
+    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(execution.input_file(params.get("obj", None)))
+    return cargs
+
+
+def dwiextract_config(
+    key: str,
+    value: str,
+) -> DwiextractConfigParamsDictTagged:
+    """
+    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 dwiextract_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractConfigParamsDict` 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 dwiextract_config_cargs(
+    params: DwiextractConfigParamsDict,
+    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 DwiextractOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DwiextractParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image (diffusion-weighted volumes by default)."""
+    export_grad_mrtrix: OutputPathType | None
+    """export the diffusion-weighted gradient table to file in MRtrix format """
+    export_grad_fsl: DwiextractExportGradFslOutputs | None
+    """Outputs from `dwiextract_export_grad_fsl_outputs`."""
+
+
+def dwiextract_params(
+    input_: InputPathType,
+    output: str,
+    bzero: bool = False,
+    no_bzero: bool = False,
+    singleshell: bool = False,
+    grad: InputPathType | None = None,
+    fslgrad: DwiextractFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: DwiextractExportGradFslParamsDict | None = None,
+    import_pe_table: InputPathType | None = None,
+    import_pe_eddy: DwiextractImportPeEddyParamsDict | None = None,
+    pe: list[float] | None = None,
+    strides: typing.Union[DwiextractVariousStringParamsDictTagged, DwiextractVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DwiextractConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DwiextractParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input DW image.
+        output: the output image (diffusion-weighted volumes by default).
+        bzero: Output b=0 volumes (instead of the diffusion weighted volumes,\
+            if -singleshell is not specified).
+        no_bzero: Output only non b=0 volumes (default, if -singleshell is not\
+            specified).
+        singleshell: Force a single-shell (single non b=0 shell) output. This\
+            will include b=0 volumes, if present. Use with -bzero to enforce\
+            presence of b=0 volumes (error if not present) or with -no_bzero to\
+            exclude them.
+        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.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        import_pe_table: import a phase-encoding table from file.
+        import_pe_eddy: import phase-encoding information from an EDDY-style\
+            config / index file pair.
+        pe: select volumes with a particular phase encoding; this can be three\
+            comma-separated values (for i,j,k components of vector direction) or\
+            four (direction & total readout time).
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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/dwiextract",
+        "bzero": bzero,
+        "no_bzero": no_bzero,
+        "singleshell": singleshell,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if shells is not None:
+        params["shells"] = shells
+    if export_grad_mrtrix is not None:
+        params["export_grad_mrtrix"] = export_grad_mrtrix
+    if export_grad_fsl is not None:
+        params["export_grad_fsl"] = export_grad_fsl
+    if import_pe_table is not None:
+        params["import_pe_table"] = import_pe_table
+    if import_pe_eddy is not None:
+        params["import_pe_eddy"] = import_pe_eddy
+    if pe is not None:
+        params["pe"] = pe
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dwiextract_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DwiextractParamsDict` 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("bzero", False) is None:
+        raise StyxValidationError("`bzero` must not be None")
+    if not isinstance(params["bzero"], bool):
+        raise StyxValidationError(f'`bzero` has the wrong type: Received `{type(params.get("bzero", False))}` expected `bool`')
+    if params.get("no_bzero", False) is None:
+        raise StyxValidationError("`no_bzero` must not be None")
+    if not isinstance(params["no_bzero"], bool):
+        raise StyxValidationError(f'`no_bzero` has the wrong type: Received `{type(params.get("no_bzero", False))}` expected `bool`')
+    if params.get("singleshell", False) is None:
+        raise StyxValidationError("`singleshell` must not be None")
+    if not isinstance(params["singleshell"], bool):
+        raise StyxValidationError(f'`singleshell` has the wrong type: Received `{type(params.get("singleshell", False))}` expected `bool`')
+    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:
+        dwiextract_fslgrad_validate(params["fslgrad"])
+    if params.get("shells", None) is not None:
+        if not isinstance(params["shells"], list):
+            raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+        for e in params["shells"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+    if params.get("export_grad_mrtrix", None) is not None:
+        if not isinstance(params["export_grad_mrtrix"], str):
+            raise StyxValidationError(f'`export_grad_mrtrix` has the wrong type: Received `{type(params.get("export_grad_mrtrix", None))}` expected `str | None`')
+    if params.get("export_grad_fsl", None) is not None:
+        dwiextract_export_grad_fsl_validate(params["export_grad_fsl"])
+    if params.get("import_pe_table", None) is not None:
+        if not isinstance(params["import_pe_table"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`import_pe_table` has the wrong type: Received `{type(params.get("import_pe_table", None))}` expected `InputPathType | None`')
+    if params.get("import_pe_eddy", None) is not None:
+        dwiextract_import_pe_eddy_validate(params["import_pe_eddy"])
+    if params.get("pe", None) is not None:
+        if not isinstance(params["pe"], list):
+            raise StyxValidationError(f'`pe` has the wrong type: Received `{type(params.get("pe", None))}` expected `list[float] | None`')
+        for e in params["pe"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`pe` has the wrong type: Received `{type(params.get("pe", None))}` expected `list[float] | None`')
+    if params.get("strides", None) is not None:
+        if not isinstance(params["strides"], dict):
+            raise StyxValidationError(f'Params object has the wrong type \'{type(params["strides"])}\'')
+        if "@type" not in params["strides"]:
+            raise StyxValidationError("Params object is missing `@type`")
+        if params["strides"]["@type"] not in ["VariousString", "VariousFile"]:
+            raise StyxValidationError("Parameter `strides`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+        dwiextract_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    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[DwiextractConfigParamsDict] | None`')
+        for e in params["config"]:
+            dwiextract_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 dwiextract_cargs(
+    params: DwiextractParamsDict,
+    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("dwiextract")
+    if params.get("bzero", False):
+        cargs.append("-bzero")
+    if params.get("no_bzero", False):
+        cargs.append("-no_bzero")
+    if params.get("singleshell", False):
+        cargs.append("-singleshell")
+    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(dwiextract_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("shells", None) is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells", None)))
+        ])
+    if params.get("export_grad_mrtrix", None) is not None:
+        cargs.extend([
+            "-export_grad_mrtrix",
+            params.get("export_grad_mrtrix", None)
+        ])
+    if params.get("export_grad_fsl", None) is not None:
+        cargs.extend(dwiextract_export_grad_fsl_cargs(params.get("export_grad_fsl", None), execution))
+    if params.get("import_pe_table", None) is not None:
+        cargs.extend([
+            "-import_pe_table",
+            execution.input_file(params.get("import_pe_table", None))
+        ])
+    if params.get("import_pe_eddy", None) is not None:
+        cargs.extend(dwiextract_import_pe_eddy_cargs(params.get("import_pe_eddy", None), execution))
+    if params.get("pe", None) is not None:
+        cargs.extend([
+            "-pe",
+            ",".join(map(str, params.get("pe", None)))
+        ])
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *dwiextract_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", 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 [dwiextract_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 dwiextract_outputs(
+    params: DwiextractParamsDict,
+    execution: Execution,
+) -> DwiextractOutputs:
+    """
+    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 = DwiextractOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+        export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix", None)) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_grad_fsl=dwiextract_export_grad_fsl_outputs(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
+    )
+    return ret
+
+
+def dwiextract_execute(
+    params: DwiextractParamsDict,
+    runner: Runner | None = None,
+) -> DwiextractOutputs:
+    """
+    dwiextract
+    
+    Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a
+    DWI dataset.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DwiextractOutputs`).
+    """
+    dwiextract_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWIEXTRACT_METADATA)
+    params = execution.params(params)
+    cargs = dwiextract_cargs(params, execution)
+    ret = dwiextract_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwiextract(
+    input_: InputPathType,
+    output: str,
+    bzero: bool = False,
+    no_bzero: bool = False,
+    singleshell: bool = False,
+    grad: InputPathType | None = None,
+    fslgrad: DwiextractFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: DwiextractExportGradFslParamsDict | None = None,
+    import_pe_table: InputPathType | None = None,
+    import_pe_eddy: DwiextractImportPeEddyParamsDict | None = None,
+    pe: list[float] | None = None,
+    strides: typing.Union[DwiextractVariousStringParamsDictTagged, DwiextractVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DwiextractConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DwiextractOutputs:
+    """
+    dwiextract
+    
+    Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a
+    DWI dataset.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input DW image.
+        output: the output image (diffusion-weighted volumes by default).
+        bzero: Output b=0 volumes (instead of the diffusion weighted volumes,\
+            if -singleshell is not specified).
+        no_bzero: Output only non b=0 volumes (default, if -singleshell is not\
+            specified).
+        singleshell: Force a single-shell (single non b=0 shell) output. This\
+            will include b=0 volumes, if present. Use with -bzero to enforce\
+            presence of b=0 volumes (error if not present) or with -no_bzero to\
+            exclude them.
+        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.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        import_pe_table: import a phase-encoding table from file.
+        import_pe_eddy: import phase-encoding information from an EDDY-style\
+            config / index file pair.
+        pe: select volumes with a particular phase encoding; this can be three\
+            comma-separated values (for i,j,k components of vector direction) or\
+            four (direction & total readout time).
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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 `DwiextractOutputs`).
+    """
+    params = dwiextract_params(
+        bzero=bzero,
+        no_bzero=no_bzero,
+        singleshell=singleshell,
+        grad=grad,
+        fslgrad=fslgrad,
+        shells=shells,
+        export_grad_mrtrix=export_grad_mrtrix,
+        export_grad_fsl=export_grad_fsl,
+        import_pe_table=import_pe_table,
+        import_pe_eddy=import_pe_eddy,
+        pe=pe,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return dwiextract_execute(params, runner)
+
+
+__all__ = [
+    "DWIEXTRACT_METADATA",
+    "DwiextractConfigParamsDict",
+    "DwiextractConfigParamsDictTagged",
+    "DwiextractExportGradFslOutputs",
+    "DwiextractExportGradFslParamsDict",
+    "DwiextractExportGradFslParamsDictTagged",
+    "DwiextractFslgradParamsDict",
+    "DwiextractFslgradParamsDictTagged",
+    "DwiextractImportPeEddyParamsDict",
+    "DwiextractImportPeEddyParamsDictTagged",
+    "DwiextractOutputs",
+    "DwiextractParamsDict",
+    "DwiextractParamsDictTagged",
+    "DwiextractVariousFileParamsDict",
+    "DwiextractVariousFileParamsDictTagged",
+    "DwiextractVariousStringParamsDict",
+    "DwiextractVariousStringParamsDictTagged",
+    "dwiextract",
+    "dwiextract_config",
+    "dwiextract_execute",
+    "dwiextract_export_grad_fsl",
+    "dwiextract_fslgrad",
+    "dwiextract_import_pe_eddy",
+    "dwiextract_params",
+    "dwiextract_various_file",
+    "dwiextract_various_string",
+]