niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwi2mask.py

@@ -0,0 +1,463 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWI2MASK_METADATA = Metadata(
+    id="e651be545db3db1ef7ebcf19117cf1ddd7e6b8f2.boutiques",
+    name="dwi2mask",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Dwi2maskFslgradParameters = typing.TypedDict('Dwi2maskFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+Dwi2maskConfigParameters = typing.TypedDict('Dwi2maskConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Dwi2maskParameters = typing.TypedDict('Dwi2maskParameters', {
+    "__STYX_TYPE__": typing.Literal["dwi2mask"],
+    "clean_scale": typing.NotRequired[int | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2maskFslgradParameters | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2maskConfigParameters] | 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 {
+        "dwi2mask": dwi2mask_cargs,
+        "fslgrad": dwi2mask_fslgrad_cargs,
+        "config": dwi2mask_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 {
+        "dwi2mask": dwi2mask_outputs,
+    }.get(t)
+
+
+def dwi2mask_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Dwi2maskFslgradParameters:
+    """
+    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 dwi2mask_fslgrad_cargs(
+    params: Dwi2maskFslgradParameters,
+    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
+
+
+def dwi2mask_config_params(
+    key: str,
+    value: str,
+) -> Dwi2maskConfigParameters:
+    """
+    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 dwi2mask_config_cargs(
+    params: Dwi2maskConfigParameters,
+    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 Dwi2maskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dwi2mask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output whole-brain mask image"""
+
+
+def dwi2mask_params(
+    input_: InputPathType,
+    output: str,
+    clean_scale: int | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2maskFslgradParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2maskConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Dwi2maskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input DWI image containing volumes that are both diffusion\
+            weighted and b=0.
+        output: the output whole-brain mask image.
+        clean_scale: the maximum scale used to cut bridges. A certain maximum\
+            scale cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            Setting this to 0 disables the mask cleaning step. (Default: 2).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dwi2mask",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if clean_scale is not None:
+        params["clean_scale"] = clean_scale
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dwi2mask_cargs(
+    params: Dwi2maskParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("dwi2mask")
+    if params.get("clean_scale") is not None:
+        cargs.extend([
+            "-clean_scale",
+            str(params.get("clean_scale"))
+        ])
+    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("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 dwi2mask_outputs(
+    params: Dwi2maskParameters,
+    execution: Execution,
+) -> Dwi2maskOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = Dwi2maskOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def dwi2mask_execute(
+    params: Dwi2maskParameters,
+    execution: Execution,
+) -> Dwi2maskOutputs:
+    """
+    Generates a whole brain mask from a DWI image.
+    
+    All diffusion weighted and b=0 volumes are used to obtain a mask that
+    includes both brain tissue and CSF.
+    
+    In a second step peninsula-like extensions, where the peninsula itself is
+    wider than the bridge connecting it to the mask, are removed. This may help
+    removing artefacts and non-brain parts, e.g. eyes, from the mask.
+    
+    References:
+    
+    Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function
+    estimation from single-shell or multi-shell diffusion MR data without a
+    co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion
+    MRI, 2016, 5.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2maskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dwi2mask_cargs(params, execution)
+    ret = dwi2mask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwi2mask(
+    input_: InputPathType,
+    output: str,
+    clean_scale: int | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2maskFslgradParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2maskConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Dwi2maskOutputs:
+    """
+    Generates a whole brain mask from a DWI image.
+    
+    All diffusion weighted and b=0 volumes are used to obtain a mask that
+    includes both brain tissue and CSF.
+    
+    In a second step peninsula-like extensions, where the peninsula itself is
+    wider than the bridge connecting it to the mask, are removed. This may help
+    removing artefacts and non-brain parts, e.g. eyes, from the mask.
+    
+    References:
+    
+    Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function
+    estimation from single-shell or multi-shell diffusion MR data without a
+    co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion
+    MRI, 2016, 5.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input DWI image containing volumes that are both diffusion\
+            weighted and b=0.
+        output: the output whole-brain mask image.
+        clean_scale: the maximum scale used to cut bridges. A certain maximum\
+            scale cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            Setting this to 0 disables the mask cleaning step. (Default: 2).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2maskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWI2MASK_METADATA)
+    params = dwi2mask_params(
+        clean_scale=clean_scale,
+        grad=grad,
+        fslgrad=fslgrad,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return dwi2mask_execute(params, execution)
+
+
+__all__ = [
+    "DWI2MASK_METADATA",
+    "Dwi2maskConfigParameters",
+    "Dwi2maskFslgradParameters",
+    "Dwi2maskOutputs",
+    "Dwi2maskParameters",
+    "dwi2mask",
+    "dwi2mask_config_params",
+    "dwi2mask_fslgrad_params",
+    "dwi2mask_params",
+]