niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrconvert.py

@@ -0,0 +1,1423 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRCONVERT_METADATA = Metadata(
+    id="698958e49f436a4dfeb7113aafd856076c1a7be7.boutiques",
+    name="mrconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrconvertCoordParameters = typing.TypedDict('MrconvertCoordParameters', {
+    "__STYX_TYPE__": typing.Literal["coord"],
+    "axis": int,
+    "selection": list[int],
+})
+
+
+MrconvertClearPropertyParameters = typing.TypedDict('MrconvertClearPropertyParameters', {
+    "__STYX_TYPE__": typing.Literal["clear_property"],
+    "key": str,
+})
+
+
+MrconvertSetPropertyParameters = typing.TypedDict('MrconvertSetPropertyParameters', {
+    "__STYX_TYPE__": typing.Literal["set_property"],
+    "key": str,
+    "value": str,
+})
+
+
+MrconvertAppendPropertyParameters = typing.TypedDict('MrconvertAppendPropertyParameters', {
+    "__STYX_TYPE__": typing.Literal["append_property"],
+    "key": str,
+    "value": str,
+})
+
+
+MrconvertVariousStringParameters = typing.TypedDict('MrconvertVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+MrconvertVariousFileParameters = typing.TypedDict('MrconvertVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+MrconvertVariousString1Parameters = typing.TypedDict('MrconvertVariousString1Parameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString_1"],
+    "obj": str,
+})
+
+
+MrconvertVariousFile1Parameters = typing.TypedDict('MrconvertVariousFile1Parameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile_1"],
+    "obj": InputPathType,
+})
+
+
+MrconvertFslgradParameters = typing.TypedDict('MrconvertFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+MrconvertExportGradFslParameters = typing.TypedDict('MrconvertExportGradFslParameters', {
+    "__STYX_TYPE__": typing.Literal["export_grad_fsl"],
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+
+
+MrconvertImportPeEddyParameters = typing.TypedDict('MrconvertImportPeEddyParameters', {
+    "__STYX_TYPE__": typing.Literal["import_pe_eddy"],
+    "config": InputPathType,
+    "indices": InputPathType,
+})
+
+
+MrconvertExportPeEddyParameters = typing.TypedDict('MrconvertExportPeEddyParameters', {
+    "__STYX_TYPE__": typing.Literal["export_pe_eddy"],
+    "config": str,
+    "indices": str,
+})
+
+
+MrconvertConfigParameters = typing.TypedDict('MrconvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrconvertParameters = typing.TypedDict('MrconvertParameters', {
+    "__STYX_TYPE__": typing.Literal["mrconvert"],
+    "coord": typing.NotRequired[list[MrconvertCoordParameters] | None],
+    "vox": typing.NotRequired[list[float] | None],
+    "axes": typing.NotRequired[list[int] | None],
+    "scaling": typing.NotRequired[list[float] | None],
+    "json_import": typing.NotRequired[InputPathType | None],
+    "json_export": typing.NotRequired[str | None],
+    "clear_property": typing.NotRequired[list[MrconvertClearPropertyParameters] | None],
+    "set_property": typing.NotRequired[list[MrconvertSetPropertyParameters] | None],
+    "append_property": typing.NotRequired[list[MrconvertAppendPropertyParameters] | None],
+    "copy_properties": typing.NotRequired[typing.Union[MrconvertVariousStringParameters, MrconvertVariousFileParameters] | None],
+    "strides": typing.NotRequired[typing.Union[MrconvertVariousString1Parameters, MrconvertVariousFile1Parameters] | None],
+    "datatype": typing.NotRequired[str | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[MrconvertFslgradParameters | None],
+    "bvalue_scaling": typing.NotRequired[str | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[MrconvertExportGradFslParameters | None],
+    "import_pe_table": typing.NotRequired[InputPathType | None],
+    "import_pe_eddy": typing.NotRequired[MrconvertImportPeEddyParameters | None],
+    "export_pe_table": typing.NotRequired[str | None],
+    "export_pe_eddy": typing.NotRequired[MrconvertExportPeEddyParameters | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrconvert": mrconvert_cargs,
+        "coord": mrconvert_coord_cargs,
+        "clear_property": mrconvert_clear_property_cargs,
+        "set_property": mrconvert_set_property_cargs,
+        "append_property": mrconvert_append_property_cargs,
+        "VariousString": mrconvert_various_string_cargs,
+        "VariousFile": mrconvert_various_file_cargs,
+        "VariousString_1": mrconvert_various_string_1_cargs,
+        "VariousFile_1": mrconvert_various_file_1_cargs,
+        "fslgrad": mrconvert_fslgrad_cargs,
+        "export_grad_fsl": mrconvert_export_grad_fsl_cargs,
+        "import_pe_eddy": mrconvert_import_pe_eddy_cargs,
+        "export_pe_eddy": mrconvert_export_pe_eddy_cargs,
+        "config": mrconvert_config_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 {
+        "mrconvert": mrconvert_outputs,
+        "export_grad_fsl": mrconvert_export_grad_fsl_outputs,
+        "export_pe_eddy": mrconvert_export_pe_eddy_outputs,
+    }.get(t)
+
+
+def mrconvert_coord_params(
+    axis: int,
+    selection: list[int],
+) -> MrconvertCoordParameters:
+    """
+    Build parameters.
+    
+    Args:
+        axis: retain data from the input image only at the coordinates\
+            specified in the selection along the specified axis. The selection\
+            argument expects a number sequence, which can also include the 'end'\
+            keyword.
+        selection: retain data from the input image only at the coordinates\
+            specified in the selection along the specified axis. The selection\
+            argument expects a number sequence, which can also include the 'end'\
+            keyword.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "coord",
+        "axis": axis,
+        "selection": selection,
+    }
+    return params
+
+
+def mrconvert_coord_cargs(
+    params: MrconvertCoordParameters,
+    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("-coord")
+    cargs.append(str(params.get("axis")))
+    cargs.extend(map(str, params.get("selection")))
+    return cargs
+
+
+def mrconvert_clear_property_params(
+    key: str,
+) -> MrconvertClearPropertyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: remove the specified key from the image header altogether.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "clear_property",
+        "key": key,
+    }
+    return params
+
+
+def mrconvert_clear_property_cargs(
+    params: MrconvertClearPropertyParameters,
+    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("-clear_property")
+    cargs.append(params.get("key"))
+    return cargs
+
+
+def mrconvert_set_property_params(
+    key: str,
+    value: str,
+) -> MrconvertSetPropertyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: set the value of the specified key in the image header.
+        value: set the value of the specified key in the image header.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "set_property",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def mrconvert_set_property_cargs(
+    params: MrconvertSetPropertyParameters,
+    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("-set_property")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+def mrconvert_append_property_params(
+    key: str,
+    value: str,
+) -> MrconvertAppendPropertyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: append the given value to the specified key in the image header\
+            (this adds the value specified as a new line in the header value).
+        value: append the given value to the specified key in the image header\
+            (this adds the value specified as a new line in the header value).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "append_property",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def mrconvert_append_property_cargs(
+    params: MrconvertAppendPropertyParameters,
+    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("-append_property")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+def mrconvert_various_string_params(
+    obj: str,
+) -> MrconvertVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def mrconvert_various_string_cargs(
+    params: MrconvertVariousStringParameters,
+    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"))
+    return cargs
+
+
+def mrconvert_various_file_params(
+    obj: InputPathType,
+) -> MrconvertVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def mrconvert_various_file_cargs(
+    params: MrconvertVariousFileParameters,
+    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")))
+    return cargs
+
+
+def mrconvert_various_string_1_params(
+    obj: str,
+) -> MrconvertVariousString1Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString_1",
+        "obj": obj,
+    }
+    return params
+
+
+def mrconvert_various_string_1_cargs(
+    params: MrconvertVariousString1Parameters,
+    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"))
+    return cargs
+
+
+def mrconvert_various_file_1_params(
+    obj: InputPathType,
+) -> MrconvertVariousFile1Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile_1",
+        "obj": obj,
+    }
+    return params
+
+
+def mrconvert_various_file_1_cargs(
+    params: MrconvertVariousFile1Parameters,
+    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")))
+    return cargs
+
+
+def mrconvert_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> MrconvertFslgradParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def mrconvert_fslgrad_cargs(
+    params: MrconvertFslgradParameters,
+    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")))
+    cargs.append(execution.input_file(params.get("bvals")))
+    return cargs
+
+
+class MrconvertExportGradFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrconvertExportGradFslParameters | 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 mrconvert_export_grad_fsl_params(
+    bvecs_path: str,
+    bvals_path: str,
+) -> MrconvertExportGradFslParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "export_grad_fsl",
+        "bvecs_path": bvecs_path,
+        "bvals_path": bvals_path,
+    }
+    return params
+
+
+def mrconvert_export_grad_fsl_cargs(
+    params: MrconvertExportGradFslParameters,
+    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"))
+    cargs.append(params.get("bvals_path"))
+    return cargs
+
+
+def mrconvert_export_grad_fsl_outputs(
+    params: MrconvertExportGradFslParameters,
+    execution: Execution,
+) -> MrconvertExportGradFslOutputs:
+    """
+    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 = MrconvertExportGradFslOutputs(
+        root=execution.output_file("."),
+        bvecs_path=execution.output_file(params.get("bvecs_path")),
+        bvals_path=execution.output_file(params.get("bvals_path")),
+    )
+    return ret
+
+
+def mrconvert_import_pe_eddy_params(
+    config: InputPathType,
+    indices: InputPathType,
+) -> MrconvertImportPeEddyParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "import_pe_eddy",
+        "config": config,
+        "indices": indices,
+    }
+    return params
+
+
+def mrconvert_import_pe_eddy_cargs(
+    params: MrconvertImportPeEddyParameters,
+    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")))
+    cargs.append(execution.input_file(params.get("indices")))
+    return cargs
+
+
+class MrconvertExportPeEddyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrconvertExportPeEddyParameters | None(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    config: OutputPathType
+    """export phase-encoding information to an EDDY-style config / index file
+    pair"""
+    indices: OutputPathType
+    """export phase-encoding information to an EDDY-style config / index file
+    pair"""
+
+
+def mrconvert_export_pe_eddy_params(
+    config: str,
+    indices: str,
+) -> MrconvertExportPeEddyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        config: export phase-encoding information to an EDDY-style config /\
+            index file pair.
+        indices: export phase-encoding information to an EDDY-style config /\
+            index file pair.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "export_pe_eddy",
+        "config": config,
+        "indices": indices,
+    }
+    return params
+
+
+def mrconvert_export_pe_eddy_cargs(
+    params: MrconvertExportPeEddyParameters,
+    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_pe_eddy")
+    cargs.append(params.get("config"))
+    cargs.append(params.get("indices"))
+    return cargs
+
+
+def mrconvert_export_pe_eddy_outputs(
+    params: MrconvertExportPeEddyParameters,
+    execution: Execution,
+) -> MrconvertExportPeEddyOutputs:
+    """
+    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 = MrconvertExportPeEddyOutputs(
+        root=execution.output_file("."),
+        config=execution.output_file(params.get("config")),
+        indices=execution.output_file(params.get("indices")),
+    )
+    return ret
+
+
+def mrconvert_config_params(
+    key: str,
+    value: str,
+) -> MrconvertConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def mrconvert_config_cargs(
+    params: MrconvertConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class MrconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrconvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+    json_export: OutputPathType | None
+    """export data from an image header key-value pairs into a JSON file """
+    export_grad_mrtrix: OutputPathType | None
+    """export the diffusion-weighted gradient table to file in MRtrix format """
+    export_pe_table: OutputPathType | None
+    """export phase-encoding table to file """
+    export_grad_fsl: MrconvertExportGradFslOutputs | None
+    """Outputs from `mrconvert_export_grad_fsl_outputs`."""
+    export_pe_eddy: MrconvertExportPeEddyOutputs | None
+    """Outputs from `mrconvert_export_pe_eddy_outputs`."""
+
+
+def mrconvert_params(
+    input_: InputPathType,
+    output: str,
+    coord: list[MrconvertCoordParameters] | None = None,
+    vox: list[float] | None = None,
+    axes: list[int] | None = None,
+    scaling: list[float] | None = None,
+    json_import: InputPathType | None = None,
+    json_export: str | None = None,
+    clear_property: list[MrconvertClearPropertyParameters] | None = None,
+    set_property: list[MrconvertSetPropertyParameters] | None = None,
+    append_property: list[MrconvertAppendPropertyParameters] | None = None,
+    copy_properties: typing.Union[MrconvertVariousStringParameters, MrconvertVariousFileParameters] | None = None,
+    strides: typing.Union[MrconvertVariousString1Parameters, MrconvertVariousFile1Parameters] | None = None,
+    datatype: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: MrconvertFslgradParameters | None = None,
+    bvalue_scaling: str | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrconvertExportGradFslParameters | None = None,
+    import_pe_table: InputPathType | None = None,
+    import_pe_eddy: MrconvertImportPeEddyParameters | None = None,
+    export_pe_table: str | None = None,
+    export_pe_eddy: MrconvertExportPeEddyParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrconvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image.
+        output: the output image.
+        coord: retain data from the input image only at the coordinates\
+            specified in the selection along the specified axis. The selection\
+            argument expects a number sequence, which can also include the 'end'\
+            keyword.
+        vox: change the voxel dimensions reported in the output image header.
+        axes: specify the axes from the input image that will be used to form\
+            the output image.
+        scaling: specify the data scaling parameters used to rescale the\
+            intensity values.
+        json_import: import data from a JSON file into header key-value pairs.
+        json_export: export data from an image header key-value pairs into a\
+            JSON file.
+        clear_property: remove the specified key from the image header\
+            altogether.
+        set_property: set the value of the specified key in the image header.
+        append_property: append the given value to the specified key in the\
+            image header (this adds the value specified as a new line in the header\
+            value).
+        copy_properties: clear all generic properties and replace with the\
+            properties from the image / file specified.
+        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.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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.
+        bvalue_scaling: enable or disable scaling of diffusion b-values by the\
+            square of the corresponding DW gradient norm (see Desciption). Valid\
+            choices are yes/no, true/false, 0/1 (default: automatic).
+        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.
+        export_pe_table: export phase-encoding table to file.
+        export_pe_eddy: export phase-encoding information to an EDDY-style\
+            config / index file pair.
+        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 = {
+        "__STYXTYPE__": "mrconvert",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if coord is not None:
+        params["coord"] = coord
+    if vox is not None:
+        params["vox"] = vox
+    if axes is not None:
+        params["axes"] = axes
+    if scaling is not None:
+        params["scaling"] = scaling
+    if json_import is not None:
+        params["json_import"] = json_import
+    if json_export is not None:
+        params["json_export"] = json_export
+    if clear_property is not None:
+        params["clear_property"] = clear_property
+    if set_property is not None:
+        params["set_property"] = set_property
+    if append_property is not None:
+        params["append_property"] = append_property
+    if copy_properties is not None:
+        params["copy_properties"] = copy_properties
+    if strides is not None:
+        params["strides"] = strides
+    if datatype is not None:
+        params["datatype"] = datatype
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if bvalue_scaling is not None:
+        params["bvalue_scaling"] = bvalue_scaling
+    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 export_pe_table is not None:
+        params["export_pe_table"] = export_pe_table
+    if export_pe_eddy is not None:
+        params["export_pe_eddy"] = export_pe_eddy
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrconvert_cargs(
+    params: MrconvertParameters,
+    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("mrconvert")
+    if params.get("coord") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("coord")] for a in c])
+    if params.get("vox") is not None:
+        cargs.extend([
+            "-vox",
+            *map(str, params.get("vox"))
+        ])
+    if params.get("axes") is not None:
+        cargs.extend([
+            "-axes",
+            ",".join(map(str, params.get("axes")))
+        ])
+    if params.get("scaling") is not None:
+        cargs.extend([
+            "-scaling",
+            *map(str, params.get("scaling"))
+        ])
+    if params.get("json_import") is not None:
+        cargs.extend([
+            "-json_import",
+            execution.input_file(params.get("json_import"))
+        ])
+    if params.get("json_export") is not None:
+        cargs.extend([
+            "-json_export",
+            params.get("json_export")
+        ])
+    if params.get("clear_property") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("clear_property")] for a in c])
+    if params.get("set_property") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("set_property")] for a in c])
+    if params.get("append_property") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("append_property")] for a in c])
+    if params.get("copy_properties") is not None:
+        cargs.extend([
+            "-copy_properties",
+            *dyn_cargs(params.get("copy_properties")["__STYXTYPE__"])(params.get("copy_properties"), execution)
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    if params.get("datatype") is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype")
+        ])
+    if params.get("grad") is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad"))
+        ])
+    if params.get("fslgrad") is not None:
+        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
+    if params.get("bvalue_scaling") is not None:
+        cargs.extend([
+            "-bvalue_scaling",
+            params.get("bvalue_scaling")
+        ])
+    if params.get("export_grad_mrtrix") is not None:
+        cargs.extend([
+            "-export_grad_mrtrix",
+            params.get("export_grad_mrtrix")
+        ])
+    if params.get("export_grad_fsl") is not None:
+        cargs.extend(dyn_cargs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution))
+    if params.get("import_pe_table") is not None:
+        cargs.extend([
+            "-import_pe_table",
+            execution.input_file(params.get("import_pe_table"))
+        ])
+    if params.get("import_pe_eddy") is not None:
+        cargs.extend(dyn_cargs(params.get("import_pe_eddy")["__STYXTYPE__"])(params.get("import_pe_eddy"), execution))
+    if params.get("export_pe_table") is not None:
+        cargs.extend([
+            "-export_pe_table",
+            params.get("export_pe_table")
+        ])
+    if params.get("export_pe_eddy") is not None:
+        cargs.extend(dyn_cargs(params.get("export_pe_eddy")["__STYXTYPE__"])(params.get("export_pe_eddy"), execution))
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrconvert_outputs(
+    params: MrconvertParameters,
+    execution: Execution,
+) -> MrconvertOutputs:
+    """
+    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 = MrconvertOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+        json_export=execution.output_file(params.get("json_export")) if (params.get("json_export") is not None) else None,
+        export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix")) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_pe_table=execution.output_file(params.get("export_pe_table")) if (params.get("export_pe_table") is not None) else None,
+        export_grad_fsl=dyn_outputs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
+        export_pe_eddy=dyn_outputs(params.get("export_pe_eddy")["__STYXTYPE__"])(params.get("export_pe_eddy"), execution) if params.get("export_pe_eddy") else None,
+    )
+    return ret
+
+
+def mrconvert_execute(
+    params: MrconvertParameters,
+    execution: Execution,
+) -> MrconvertOutputs:
+    """
+    Perform conversion between different file types and optionally extract a subset
+    of the input image.
+    
+    If used correctly, this program can be a very useful workhorse. In addition
+    to converting images between different formats, it can be used to extract
+    specific studies from a data set, extract a specific region of interest, or
+    flip the images. Some of the possible operations are described in more
+    detail below.
+    
+    Note that for both the -coord and -axes options, indexing starts from 0
+    rather than 1. E.g. -coord 3 <#> selects volumes (the fourth dimension) from
+    the series; -axes 0,1,2 includes only the three spatial axes in the output
+    image.
+    
+    Additionally, for the second input to the -coord option and the -axes
+    option, you can use any valid number sequence in the selection, as well as
+    the 'end' keyword (see the main documentation for details); this can be
+    particularly useful to select multiple coordinates.
+    
+    The -vox option is used to change the size of the voxels in the output image
+    as reported in the image header; note however that this does not re-sample
+    the image based on a new voxel size (that is done using the mrgrid command).
+    
+    By default, the intensity scaling parameters in the input image header are
+    passed through to the output image header when writing to an integer image,
+    and reset to 0,1 (i.e. no scaling) for floating-point and binary images.
+    Note that the -scaling option will therefore have no effect for
+    floating-point or binary output images.
+    
+    The -axes option specifies which axes from the input image will be used to
+    form the output image. This allows the permutation, omission, or addition of
+    axes into the output image. The axes should be supplied as a comma-separated
+    list of axis indices. If an axis from the input image is to be omitted from
+    the output image, it must either already have a size of 1, or a single
+    coordinate along that axis must be selected by the user by using the -coord
+    option. Examples are provided further below.
+    
+    The -bvalue_scaling option controls an aspect of the import of diffusion
+    gradient tables. When the input diffusion-weighting direction vectors have
+    norms that differ substantially from unity, the b-values will be scaled by
+    the square of their corresponding vector norm (this is how multi-shell
+    acquisitions are frequently achieved on scanner platforms). However in some
+    rare instances, the b-values may be correct, despite the vectors not being
+    of unit norm (or conversely, the b-values may need to be rescaled even
+    though the vectors are close to unit norm). This option allows the user to
+    control this operation and override MRrtix3's automatic detection.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrconvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrconvert_cargs(params, execution)
+    ret = mrconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrconvert(
+    input_: InputPathType,
+    output: str,
+    coord: list[MrconvertCoordParameters] | None = None,
+    vox: list[float] | None = None,
+    axes: list[int] | None = None,
+    scaling: list[float] | None = None,
+    json_import: InputPathType | None = None,
+    json_export: str | None = None,
+    clear_property: list[MrconvertClearPropertyParameters] | None = None,
+    set_property: list[MrconvertSetPropertyParameters] | None = None,
+    append_property: list[MrconvertAppendPropertyParameters] | None = None,
+    copy_properties: typing.Union[MrconvertVariousStringParameters, MrconvertVariousFileParameters] | None = None,
+    strides: typing.Union[MrconvertVariousString1Parameters, MrconvertVariousFile1Parameters] | None = None,
+    datatype: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: MrconvertFslgradParameters | None = None,
+    bvalue_scaling: str | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrconvertExportGradFslParameters | None = None,
+    import_pe_table: InputPathType | None = None,
+    import_pe_eddy: MrconvertImportPeEddyParameters | None = None,
+    export_pe_table: str | None = None,
+    export_pe_eddy: MrconvertExportPeEddyParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrconvertOutputs:
+    """
+    Perform conversion between different file types and optionally extract a subset
+    of the input image.
+    
+    If used correctly, this program can be a very useful workhorse. In addition
+    to converting images between different formats, it can be used to extract
+    specific studies from a data set, extract a specific region of interest, or
+    flip the images. Some of the possible operations are described in more
+    detail below.
+    
+    Note that for both the -coord and -axes options, indexing starts from 0
+    rather than 1. E.g. -coord 3 <#> selects volumes (the fourth dimension) from
+    the series; -axes 0,1,2 includes only the three spatial axes in the output
+    image.
+    
+    Additionally, for the second input to the -coord option and the -axes
+    option, you can use any valid number sequence in the selection, as well as
+    the 'end' keyword (see the main documentation for details); this can be
+    particularly useful to select multiple coordinates.
+    
+    The -vox option is used to change the size of the voxels in the output image
+    as reported in the image header; note however that this does not re-sample
+    the image based on a new voxel size (that is done using the mrgrid command).
+    
+    By default, the intensity scaling parameters in the input image header are
+    passed through to the output image header when writing to an integer image,
+    and reset to 0,1 (i.e. no scaling) for floating-point and binary images.
+    Note that the -scaling option will therefore have no effect for
+    floating-point or binary output images.
+    
+    The -axes option specifies which axes from the input image will be used to
+    form the output image. This allows the permutation, omission, or addition of
+    axes into the output image. The axes should be supplied as a comma-separated
+    list of axis indices. If an axis from the input image is to be omitted from
+    the output image, it must either already have a size of 1, or a single
+    coordinate along that axis must be selected by the user by using the -coord
+    option. Examples are provided further below.
+    
+    The -bvalue_scaling option controls an aspect of the import of diffusion
+    gradient tables. When the input diffusion-weighting direction vectors have
+    norms that differ substantially from unity, the b-values will be scaled by
+    the square of their corresponding vector norm (this is how multi-shell
+    acquisitions are frequently achieved on scanner platforms). However in some
+    rare instances, the b-values may be correct, despite the vectors not being
+    of unit norm (or conversely, the b-values may need to be rescaled even
+    though the vectors are close to unit norm). This option allows the user to
+    control this operation and override MRrtix3's automatic detection.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image.
+        output: the output image.
+        coord: retain data from the input image only at the coordinates\
+            specified in the selection along the specified axis. The selection\
+            argument expects a number sequence, which can also include the 'end'\
+            keyword.
+        vox: change the voxel dimensions reported in the output image header.
+        axes: specify the axes from the input image that will be used to form\
+            the output image.
+        scaling: specify the data scaling parameters used to rescale the\
+            intensity values.
+        json_import: import data from a JSON file into header key-value pairs.
+        json_export: export data from an image header key-value pairs into a\
+            JSON file.
+        clear_property: remove the specified key from the image header\
+            altogether.
+        set_property: set the value of the specified key in the image header.
+        append_property: append the given value to the specified key in the\
+            image header (this adds the value specified as a new line in the header\
+            value).
+        copy_properties: clear all generic properties and replace with the\
+            properties from the image / file specified.
+        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.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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.
+        bvalue_scaling: enable or disable scaling of diffusion b-values by the\
+            square of the corresponding DW gradient norm (see Desciption). Valid\
+            choices are yes/no, true/false, 0/1 (default: automatic).
+        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.
+        export_pe_table: export phase-encoding table to file.
+        export_pe_eddy: export phase-encoding information to an EDDY-style\
+            config / index file pair.
+        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 `MrconvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCONVERT_METADATA)
+    params = mrconvert_params(
+        coord=coord,
+        vox=vox,
+        axes=axes,
+        scaling=scaling,
+        json_import=json_import,
+        json_export=json_export,
+        clear_property=clear_property,
+        set_property=set_property,
+        append_property=append_property,
+        copy_properties=copy_properties,
+        strides=strides,
+        datatype=datatype,
+        grad=grad,
+        fslgrad=fslgrad,
+        bvalue_scaling=bvalue_scaling,
+        export_grad_mrtrix=export_grad_mrtrix,
+        export_grad_fsl=export_grad_fsl,
+        import_pe_table=import_pe_table,
+        import_pe_eddy=import_pe_eddy,
+        export_pe_table=export_pe_table,
+        export_pe_eddy=export_pe_eddy,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return mrconvert_execute(params, execution)
+
+
+__all__ = [
+    "MRCONVERT_METADATA",
+    "MrconvertAppendPropertyParameters",
+    "MrconvertClearPropertyParameters",
+    "MrconvertConfigParameters",
+    "MrconvertCoordParameters",
+    "MrconvertExportGradFslOutputs",
+    "MrconvertExportGradFslParameters",
+    "MrconvertExportPeEddyOutputs",
+    "MrconvertExportPeEddyParameters",
+    "MrconvertFslgradParameters",
+    "MrconvertImportPeEddyParameters",
+    "MrconvertOutputs",
+    "MrconvertParameters",
+    "MrconvertSetPropertyParameters",
+    "MrconvertVariousFile1Parameters",
+    "MrconvertVariousFileParameters",
+    "MrconvertVariousString1Parameters",
+    "MrconvertVariousStringParameters",
+    "mrconvert",
+    "mrconvert_append_property_params",
+    "mrconvert_clear_property_params",
+    "mrconvert_config_params",
+    "mrconvert_coord_params",
+    "mrconvert_export_grad_fsl_params",
+    "mrconvert_export_pe_eddy_params",
+    "mrconvert_fslgrad_params",
+    "mrconvert_import_pe_eddy_params",
+    "mrconvert_params",
+    "mrconvert_set_property_params",
+    "mrconvert_various_file_1_params",
+    "mrconvert_various_file_params",
+    "mrconvert_various_string_1_params",
+    "mrconvert_various_string_params",
+]