niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/afdconnectivity.py

@@ -0,0 +1,527 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFDCONNECTIVITY_METADATA = Metadata(
+    id="a6fb5580a7faf6e50bbcf57a2c6385623c779645.boutiques",
+    name="afdconnectivity",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_AfdconnectivityConfigParamsDictNoTag = typing.TypedDict('_AfdconnectivityConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+AfdconnectivityConfigParamsDictTagged = typing.TypedDict('AfdconnectivityConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+AfdconnectivityConfigParamsDict = _AfdconnectivityConfigParamsDictNoTag | AfdconnectivityConfigParamsDictTagged
+
+
+_AfdconnectivityParamsDictNoTag = typing.TypedDict('_AfdconnectivityParamsDictNoTag', {
+    "wbft": typing.NotRequired[InputPathType | None],
+    "afd_map": typing.NotRequired[str | None],
+    "all_fixels": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[AfdconnectivityConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+    "tracks": InputPathType,
+})
+AfdconnectivityParamsDictTagged = typing.TypedDict('AfdconnectivityParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/afdconnectivity"],
+    "wbft": typing.NotRequired[InputPathType | None],
+    "afd_map": typing.NotRequired[str | None],
+    "all_fixels": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[AfdconnectivityConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+    "tracks": InputPathType,
+})
+AfdconnectivityParamsDict = _AfdconnectivityParamsDictNoTag | AfdconnectivityParamsDictTagged
+
+
+def afdconnectivity_config(
+    key: str,
+    value: str,
+) -> AfdconnectivityConfigParamsDictTagged:
+    """
+    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 afdconnectivity_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `AfdconnectivityConfigParamsDict` 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 afdconnectivity_config_cargs(
+    params: AfdconnectivityConfigParamsDict,
+    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 AfdconnectivityOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `AfdconnectivityParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    afd_map: OutputPathType | None
+    """output a 3D image containing the AFD estimated for each voxel. """
+
+
+def afdconnectivity_params(
+    image: InputPathType,
+    tracks: InputPathType,
+    wbft: InputPathType | None = None,
+    afd_map: str | None = None,
+    all_fixels: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[AfdconnectivityConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> AfdconnectivityParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        image: the input FOD image.
+        tracks: the input track file defining the bundle of interest.
+        wbft: provide a whole-brain fibre-tracking data set (of which the input\
+            track file should be a subset), to improve the estimate of fibre bundle\
+            volume in the presence of partial volume.
+        afd_map: output a 3D image containing the AFD estimated for each voxel.
+        all_fixels: if whole-brain fibre-tracking is NOT provided, then if\
+            multiple fixels within a voxel are traversed by the pathway of\
+            interest, by default the fixel with the greatest streamlines density is\
+            selected to contribute to the AFD in that voxel. If this option is\
+            provided, then ALL fixels with non-zero streamlines density will\
+            contribute to the result, even if multiple fixels per voxel are\
+            selected.
+        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/afdconnectivity",
+        "all_fixels": all_fixels,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "image": image,
+        "tracks": tracks,
+    }
+    if wbft is not None:
+        params["wbft"] = wbft
+    if afd_map is not None:
+        params["afd_map"] = afd_map
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def afdconnectivity_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `AfdconnectivityParamsDict` 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("wbft", None) is not None:
+        if not isinstance(params["wbft"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`wbft` has the wrong type: Received `{type(params.get("wbft", None))}` expected `InputPathType | None`')
+    if params.get("afd_map", None) is not None:
+        if not isinstance(params["afd_map"], str):
+            raise StyxValidationError(f'`afd_map` has the wrong type: Received `{type(params.get("afd_map", None))}` expected `str | None`')
+    if params.get("all_fixels", False) is None:
+        raise StyxValidationError("`all_fixels` must not be None")
+    if not isinstance(params["all_fixels"], bool):
+        raise StyxValidationError(f'`all_fixels` has the wrong type: Received `{type(params.get("all_fixels", False))}` expected `bool`')
+    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[AfdconnectivityConfigParamsDict] | None`')
+        for e in params["config"]:
+            afdconnectivity_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("image", None) is None:
+        raise StyxValidationError("`image` must not be None")
+    if not isinstance(params["image"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `InputPathType`')
+    if params.get("tracks", None) is None:
+        raise StyxValidationError("`tracks` must not be None")
+    if not isinstance(params["tracks"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks` has the wrong type: Received `{type(params.get("tracks", None))}` expected `InputPathType`')
+
+
+def afdconnectivity_cargs(
+    params: AfdconnectivityParamsDict,
+    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("afdconnectivity")
+    if params.get("wbft", None) is not None:
+        cargs.extend([
+            "-wbft",
+            execution.input_file(params.get("wbft", None))
+        ])
+    if params.get("afd_map", None) is not None:
+        cargs.extend([
+            "-afd_map",
+            params.get("afd_map", None)
+        ])
+    if params.get("all_fixels", False):
+        cargs.append("-all_fixels")
+    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 [afdconnectivity_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("image", None)))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    return cargs
+
+
+def afdconnectivity_outputs(
+    params: AfdconnectivityParamsDict,
+    execution: Execution,
+) -> AfdconnectivityOutputs:
+    """
+    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 = AfdconnectivityOutputs(
+        root=execution.output_file("."),
+        afd_map=execution.output_file(params.get("afd_map", None)) if (params.get("afd_map") is not None) else None,
+    )
+    return ret
+
+
+def afdconnectivity_execute(
+    params: AfdconnectivityParamsDict,
+    runner: Runner | None = None,
+) -> AfdconnectivityOutputs:
+    """
+    afdconnectivity
+    
+    Obtain an estimate of fibre connectivity between two regions using AFD and
+    streamlines tractography.
+    
+    This estimate is obtained by determining a fibre volume (AFD) occupied by
+    the pathway of interest, and dividing by the streamline length.
+    
+    If only the streamlines belonging to the pathway of interest are provided,
+    then ALL of the fibre volume within each fixel selected will contribute to
+    the result. If the -wbft option is used to provide whole-brain
+    fibre-tracking (of which the pathway of interest should contain a subset),
+    only the fraction of the fibre volume in each fixel estimated to belong to
+    the pathway of interest will contribute to the result.
+    
+    Use -quiet to suppress progress messages and output fibre connectivity value
+    only.
+    
+    For valid comparisons of AFD connectivity across scans, images MUST be
+    intensity normalised and bias field corrected, and a common response
+    function for all subjects must be used.
+    
+    Note that the sum of the AFD is normalised by streamline length to account
+    for subject differences in fibre bundle length. This normalisation results
+    in a measure that is more related to the cross-sectional volume of the tract
+    (and therefore 'connectivity'). Note that SIFT-ed tract count is a superior
+    measure because it is unaffected by tangential yet unrelated fibres.
+    However, AFD connectivity may be used as a substitute when Anatomically
+    Constrained Tractography is not possible due to uncorrectable EPI
+    distortions, and SIFT may therefore not be as effective.
+    
+    Longer discussion regarding this command can additionally be found at:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/afd_connectivity.html (as
+    well as in the relevant reference).
+    
+    References:
+    
+    Smith, R. E.; Raffelt, D.; Tournier, J.-D.; Connelly, A. Quantitative
+    Streamlines Tractography: Methods and Inter-Subject Normalisation. Open
+    Science Framework, https://doi.org/10.31219/osf.io/c67kn.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AfdconnectivityOutputs`).
+    """
+    afdconnectivity_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFDCONNECTIVITY_METADATA)
+    params = execution.params(params)
+    cargs = afdconnectivity_cargs(params, execution)
+    ret = afdconnectivity_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def afdconnectivity(
+    image: InputPathType,
+    tracks: InputPathType,
+    wbft: InputPathType | None = None,
+    afd_map: str | None = None,
+    all_fixels: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[AfdconnectivityConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> AfdconnectivityOutputs:
+    """
+    afdconnectivity
+    
+    Obtain an estimate of fibre connectivity between two regions using AFD and
+    streamlines tractography.
+    
+    This estimate is obtained by determining a fibre volume (AFD) occupied by
+    the pathway of interest, and dividing by the streamline length.
+    
+    If only the streamlines belonging to the pathway of interest are provided,
+    then ALL of the fibre volume within each fixel selected will contribute to
+    the result. If the -wbft option is used to provide whole-brain
+    fibre-tracking (of which the pathway of interest should contain a subset),
+    only the fraction of the fibre volume in each fixel estimated to belong to
+    the pathway of interest will contribute to the result.
+    
+    Use -quiet to suppress progress messages and output fibre connectivity value
+    only.
+    
+    For valid comparisons of AFD connectivity across scans, images MUST be
+    intensity normalised and bias field corrected, and a common response
+    function for all subjects must be used.
+    
+    Note that the sum of the AFD is normalised by streamline length to account
+    for subject differences in fibre bundle length. This normalisation results
+    in a measure that is more related to the cross-sectional volume of the tract
+    (and therefore 'connectivity'). Note that SIFT-ed tract count is a superior
+    measure because it is unaffected by tangential yet unrelated fibres.
+    However, AFD connectivity may be used as a substitute when Anatomically
+    Constrained Tractography is not possible due to uncorrectable EPI
+    distortions, and SIFT may therefore not be as effective.
+    
+    Longer discussion regarding this command can additionally be found at:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/afd_connectivity.html (as
+    well as in the relevant reference).
+    
+    References:
+    
+    Smith, R. E.; Raffelt, D.; Tournier, J.-D.; Connelly, A. Quantitative
+    Streamlines Tractography: Methods and Inter-Subject Normalisation. Open
+    Science Framework, https://doi.org/10.31219/osf.io/c67kn.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        image: the input FOD image.
+        tracks: the input track file defining the bundle of interest.
+        wbft: provide a whole-brain fibre-tracking data set (of which the input\
+            track file should be a subset), to improve the estimate of fibre bundle\
+            volume in the presence of partial volume.
+        afd_map: output a 3D image containing the AFD estimated for each voxel.
+        all_fixels: if whole-brain fibre-tracking is NOT provided, then if\
+            multiple fixels within a voxel are traversed by the pathway of\
+            interest, by default the fixel with the greatest streamlines density is\
+            selected to contribute to the AFD in that voxel. If this option is\
+            provided, then ALL fixels with non-zero streamlines density will\
+            contribute to the result, even if multiple fixels per voxel are\
+            selected.
+        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 `AfdconnectivityOutputs`).
+    """
+    params = afdconnectivity_params(
+        wbft=wbft,
+        afd_map=afd_map,
+        all_fixels=all_fixels,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        image=image,
+        tracks=tracks,
+    )
+    return afdconnectivity_execute(params, runner)
+
+
+__all__ = [
+    "AFDCONNECTIVITY_METADATA",
+    "AfdconnectivityConfigParamsDict",
+    "AfdconnectivityConfigParamsDictTagged",
+    "AfdconnectivityOutputs",
+    "AfdconnectivityParamsDict",
+    "AfdconnectivityParamsDictTagged",
+    "afdconnectivity",
+    "afdconnectivity_config",
+    "afdconnectivity_execute",
+    "afdconnectivity_params",
+]