niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/__init__.py

@@ -0,0 +1,130 @@
+"""
+MRTrix3
+
+MRtrix3 provides a set of tools to perform various types of diffusion MRI
+analyses, from various forms of tractography through to next-generation
+group-level analyses. It is designed with consistency, performance, and
+stability in mind, and is freely available under an open-source license. It is
+developed and maintained by a team of experts in the field, fostering an active
+community of users from diverse backgrounds.
+
+URL: https://www.mrtrix.org/
+"""
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+from .afdconnectivity import *
+from .amp2response import *
+from .amp2sh import *
+from .connectome2tck import *
+from .connectomeedit import *
+from .connectomestats import *
+from .dcmedit import *
+from .dcminfo import *
+from .dirflip import *
+from .dirgen import *
+from .dirmerge import *
+from .dirorder import *
+from .dirsplit import *
+from .dirstat import *
+from .dwi2adc import *
+from .dwi2fod import *
+from .dwi2mask import *
+from .dwi2response import *
+from .dwi2tensor import *
+from .dwibiascorrect import *
+from .dwidenoise import *
+from .dwiextract import *
+from .dwigradcheck import *
+from .fixel2peaks import *
+from .fixel2sh import *
+from .fixel2tsf import *
+from .fixel2voxel import *
+from .fixelcfestats import *
+from .fixelconnectivity import *
+from .fixelconvert import *
+from .fixelcorrespondence import *
+from .fixelcrop import *
+from .fixelfilter import *
+from .fixelreorient import *
+from .fod2dec import *
+from .fod2fixel import *
+from .label2colour import *
+from .label2mesh import *
+from .labelconvert import *
+from .labelstats import *
+from .maskdump import *
+from .maskfilter import *
+from .mesh2voxel import *
+from .meshconvert import *
+from .meshfilter import *
+from .mraverageheader import *
+from .mrcalc import *
+from .mrcat import *
+from .mrcentroid import *
+from .mrcheckerboardmask import *
+from .mrclusterstats import *
+from .mrcolour import *
+from .mrconvert import *
+from .mrdegibbs import *
+from .mrdump import *
+from .mredit import *
+from .mrfilter import *
+from .mrgrid import *
+from .mrhistmatch import *
+from .mrhistogram import *
+from .mrinfo import *
+from .mrmath import *
+from .mrmetric import *
+from .mrregister import *
+from .mrstats import *
+from .mrthreshold import *
+from .mrtransform import *
+from .mtnormalise import *
+from .peaks2amp import *
+from .peaks2fixel import *
+from .responsemean import *
+from .sh2amp import *
+from .sh2peaks import *
+from .sh2power import *
+from .sh2response import *
+from .shbasis import *
+from .shconv import *
+from .tck2connectome import *
+from .tck2fixel import *
+from .tckconvert import *
+from .tckdfc import *
+from .tckedit import *
+from .tckgen import *
+from .tckglobal import *
+from .tckinfo import *
+from .tckmap import *
+from .tckresample import *
+from .tcksample import *
+from .tcksift import *
+from .tcksift2 import *
+from .tckstats import *
+from .tcktransform import *
+from .tensor2metric import *
+from .transformcalc import *
+from .transformcompose import *
+from .transformconvert import *
+from .tsfdivide import *
+from .tsfinfo import *
+from .tsfmult import *
+from .tsfsmooth import *
+from .tsfthreshold import *
+from .tsfvalidate import *
+from .v_5tt2gmwmi import *
+from .v_5tt2vis import *
+from .v_5ttcheck import *
+from .v_5ttedit import *
+from .v_5ttgen import *
+from .vectorstats import *
+from .voxel2fixel import *
+from .voxel2mesh import *
+from .warp2metric import *
+from .warpconvert import *
+from .warpcorrect import *
+from .warpinit import *
+from .warpinvert import *

niwrap_mrtrix/mrtrix/afdconnectivity.py

@@ -0,0 +1,445 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AFDCONNECTIVITY_METADATA = Metadata(
+    id="3290302704162d6eadb785f29be4535da532166f.boutiques",
+    name="afdconnectivity",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+AfdconnectivityConfigParameters = typing.TypedDict('AfdconnectivityConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+AfdconnectivityParameters = typing.TypedDict('AfdconnectivityParameters', {
+    "__STYX_TYPE__": typing.Literal["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[AfdconnectivityConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+    "tracks": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "afdconnectivity": afdconnectivity_cargs,
+        "config": afdconnectivity_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 {
+        "afdconnectivity": afdconnectivity_outputs,
+    }.get(t)
+
+
+def afdconnectivity_config_params(
+    key: str,
+    value: str,
+) -> AfdconnectivityConfigParameters:
+    """
+    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 afdconnectivity_config_cargs(
+    params: AfdconnectivityConfigParameters,
+    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 AfdconnectivityOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `afdconnectivity(...)`.
+    """
+    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[AfdconnectivityConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> AfdconnectivityParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: AfdconnectivityParameters,
+    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") is not None:
+        cargs.extend([
+            "-wbft",
+            execution.input_file(params.get("wbft"))
+        ])
+    if params.get("afd_map") is not None:
+        cargs.extend([
+            "-afd_map",
+            params.get("afd_map")
+        ])
+    if params.get("all_fixels"):
+        cargs.append("-all_fixels")
+    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("image")))
+    cargs.append(execution.input_file(params.get("tracks")))
+    return cargs
+
+
+def afdconnectivity_outputs(
+    params: AfdconnectivityParameters,
+    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")) if (params.get("afd_map") is not None) else None,
+    )
+    return ret
+
+
+def afdconnectivity_execute(
+    params: AfdconnectivityParameters,
+    execution: Execution,
+) -> AfdconnectivityOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AfdconnectivityOutputs`).
+    """
+    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[AfdconnectivityConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> AfdconnectivityOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFDCONNECTIVITY_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "AFDCONNECTIVITY_METADATA",
+    "AfdconnectivityConfigParameters",
+    "AfdconnectivityOutputs",
+    "AfdconnectivityParameters",
+    "afdconnectivity",
+    "afdconnectivity_config_params",
+    "afdconnectivity_params",
+]