niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckdfc.py

@@ -0,0 +1,551 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKDFC_METADATA = Metadata(
+    id="9ecab23d43de088c2cabc9280d7379293cf1dc28.boutiques",
+    name="tckdfc",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TckdfcDynamicParameters = typing.TypedDict('TckdfcDynamicParameters', {
+    "__STYX_TYPE__": typing.Literal["dynamic"],
+    "shape": str,
+    "width": int,
+})
+
+
+TckdfcConfigParameters = typing.TypedDict('TckdfcConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TckdfcParameters = typing.TypedDict('TckdfcParameters', {
+    "__STYX_TYPE__": typing.Literal["tckdfc"],
+    "static": bool,
+    "dynamic": typing.NotRequired[TckdfcDynamicParameters | None],
+    "template": typing.NotRequired[InputPathType | None],
+    "vox": typing.NotRequired[list[float] | None],
+    "stat_vox": typing.NotRequired[str | None],
+    "backtrack": bool,
+    "upsample": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckdfcConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "fmri": 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 {
+        "tckdfc": tckdfc_cargs,
+        "dynamic": tckdfc_dynamic_cargs,
+        "config": tckdfc_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 {
+        "tckdfc": tckdfc_outputs,
+    }.get(t)
+
+
+def tckdfc_dynamic_params(
+    shape: str,
+    width: int,
+) -> TckdfcDynamicParameters:
+    """
+    Build parameters.
+    
+    Args:
+        shape: generate a "dynamic" (4D) output image; must additionally\
+            provide the shape and width (in volumes) of the sliding window.
+        width: generate a "dynamic" (4D) output image; must additionally\
+            provide the shape and width (in volumes) of the sliding window.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dynamic",
+        "shape": shape,
+        "width": width,
+    }
+    return params
+
+
+def tckdfc_dynamic_cargs(
+    params: TckdfcDynamicParameters,
+    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("-dynamic")
+    cargs.append(params.get("shape"))
+    cargs.append(str(params.get("width")))
+    return cargs
+
+
+def tckdfc_config_params(
+    key: str,
+    value: str,
+) -> TckdfcConfigParameters:
+    """
+    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 tckdfc_config_cargs(
+    params: TckdfcConfigParameters,
+    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 TckdfcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tckdfc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output TW-dFC image"""
+
+
+def tckdfc_params(
+    tracks: InputPathType,
+    fmri: InputPathType,
+    output: str,
+    static: bool = False,
+    dynamic: TckdfcDynamicParameters | None = None,
+    template: InputPathType | None = None,
+    vox: list[float] | None = None,
+    stat_vox: str | None = None,
+    backtrack: bool = False,
+    upsample: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckdfcConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckdfcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tracks: the input track file.
+        fmri: the pre-processed fMRI time series.
+        output: the output TW-dFC image.
+        static: generate a "static" (3D) output image.
+        dynamic: generate a "dynamic" (4D) output image; must additionally\
+            provide the shape and width (in volumes) of the sliding window.
+        template: an image file to be used as a template for the output (the\
+            output image will have the same transform and field of view).
+        vox: provide either an isotropic voxel size (in mm), or comma-separated\
+            list of 3 voxel dimensions.
+        stat_vox: define the statistic for choosing the final voxel intensities\
+            for a given contrast type given the individual values from the tracks\
+            passing through each voxel\
+            Options are: sum, min, mean, max (default: mean).
+        backtrack: if no valid timeseries is found at the streamline endpoint,\
+            back-track along the streamline trajectory until a valid timeseries is\
+            found.
+        upsample: upsample the tracks by some ratio using Hermite interpolation\
+            before mapping (if omitted, an appropriate ratio will be determined\
+            automatically).
+        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__": "tckdfc",
+        "static": static,
+        "backtrack": backtrack,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks": tracks,
+        "fmri": fmri,
+        "output": output,
+    }
+    if dynamic is not None:
+        params["dynamic"] = dynamic
+    if template is not None:
+        params["template"] = template
+    if vox is not None:
+        params["vox"] = vox
+    if stat_vox is not None:
+        params["stat_vox"] = stat_vox
+    if upsample is not None:
+        params["upsample"] = upsample
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckdfc_cargs(
+    params: TckdfcParameters,
+    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("tckdfc")
+    if params.get("static"):
+        cargs.append("-static")
+    if params.get("dynamic") is not None:
+        cargs.extend(dyn_cargs(params.get("dynamic")["__STYXTYPE__"])(params.get("dynamic"), execution))
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    if params.get("vox") is not None:
+        cargs.extend([
+            "-vox",
+            ",".join(map(str, params.get("vox")))
+        ])
+    if params.get("stat_vox") is not None:
+        cargs.extend([
+            "-stat_vox",
+            params.get("stat_vox")
+        ])
+    if params.get("backtrack"):
+        cargs.append("-backtrack")
+    if params.get("upsample") is not None:
+        cargs.extend([
+            "-upsample",
+            str(params.get("upsample"))
+        ])
+    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("tracks")))
+    cargs.append(execution.input_file(params.get("fmri")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def tckdfc_outputs(
+    params: TckdfcParameters,
+    execution: Execution,
+) -> TckdfcOutputs:
+    """
+    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 = TckdfcOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def tckdfc_execute(
+    params: TckdfcParameters,
+    execution: Execution,
+) -> TckdfcOutputs:
+    """
+    Perform the Track-Weighted Dynamic Functional Connectivity (TW-dFC) method.
+    
+    This command generates a Track-Weighted Image (TWI), where the contribution
+    from each streamline to the image is the Pearson correlation between the
+    fMRI time series at the streamline endpoints.
+    
+    The output image can be generated in one of two ways (note that one of these
+    two command-line options MUST be provided):
+    
+    - "Static" functional connectivity (-static option): Each streamline
+    contributes to a static 3D output image based on the correlation between the
+    signals at the streamline endpoints using the entirety of the input time
+    series.
+    
+    - "Dynamic" functional connectivity (-dynamic option): The output image is a
+    4D image, with the same number of volumes as the input fMRI time series. For
+    each volume, the contribution from each streamline is calculated based on a
+    finite-width sliding time window, centred at the timepoint corresponding to
+    that volume.
+    
+    Note that the -backtrack option in this command is similar, but not
+    precisely equivalent, to back-tracking as can be used with
+    Anatomically-Constrained Tractography (ACT) in the tckgen command. However,
+    here the feature does not change the streamlines trajectories in any way; it
+    simply enables detection of the fact that the input fMRI image may not
+    contain a valid timeseries underneath the streamline endpoint, and where
+    this occurs, searches from the streamline endpoint inwards along the
+    streamline trajectory in search of a valid timeseries to sample from the
+    input image.
+    
+    References:
+    
+    Calamante, F.; Smith, R.E.; Liang, X.; Zalesky, A.; Connelly, A
+    Track-weighted dynamic functional connectivity (TW-dFC): a new method to
+    study time-resolved functional connectivity. Brain Struct Funct, 2017, doi:
+    10.1007/s00429-017-1431-1.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TckdfcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tckdfc_cargs(params, execution)
+    ret = tckdfc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckdfc(
+    tracks: InputPathType,
+    fmri: InputPathType,
+    output: str,
+    static: bool = False,
+    dynamic: TckdfcDynamicParameters | None = None,
+    template: InputPathType | None = None,
+    vox: list[float] | None = None,
+    stat_vox: str | None = None,
+    backtrack: bool = False,
+    upsample: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckdfcConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckdfcOutputs:
+    """
+    Perform the Track-Weighted Dynamic Functional Connectivity (TW-dFC) method.
+    
+    This command generates a Track-Weighted Image (TWI), where the contribution
+    from each streamline to the image is the Pearson correlation between the
+    fMRI time series at the streamline endpoints.
+    
+    The output image can be generated in one of two ways (note that one of these
+    two command-line options MUST be provided):
+    
+    - "Static" functional connectivity (-static option): Each streamline
+    contributes to a static 3D output image based on the correlation between the
+    signals at the streamline endpoints using the entirety of the input time
+    series.
+    
+    - "Dynamic" functional connectivity (-dynamic option): The output image is a
+    4D image, with the same number of volumes as the input fMRI time series. For
+    each volume, the contribution from each streamline is calculated based on a
+    finite-width sliding time window, centred at the timepoint corresponding to
+    that volume.
+    
+    Note that the -backtrack option in this command is similar, but not
+    precisely equivalent, to back-tracking as can be used with
+    Anatomically-Constrained Tractography (ACT) in the tckgen command. However,
+    here the feature does not change the streamlines trajectories in any way; it
+    simply enables detection of the fact that the input fMRI image may not
+    contain a valid timeseries underneath the streamline endpoint, and where
+    this occurs, searches from the streamline endpoint inwards along the
+    streamline trajectory in search of a valid timeseries to sample from the
+    input image.
+    
+    References:
+    
+    Calamante, F.; Smith, R.E.; Liang, X.; Zalesky, A.; Connelly, A
+    Track-weighted dynamic functional connectivity (TW-dFC): a new method to
+    study time-resolved functional connectivity. Brain Struct Funct, 2017, doi:
+    10.1007/s00429-017-1431-1.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks: the input track file.
+        fmri: the pre-processed fMRI time series.
+        output: the output TW-dFC image.
+        static: generate a "static" (3D) output image.
+        dynamic: generate a "dynamic" (4D) output image; must additionally\
+            provide the shape and width (in volumes) of the sliding window.
+        template: an image file to be used as a template for the output (the\
+            output image will have the same transform and field of view).
+        vox: provide either an isotropic voxel size (in mm), or comma-separated\
+            list of 3 voxel dimensions.
+        stat_vox: define the statistic for choosing the final voxel intensities\
+            for a given contrast type given the individual values from the tracks\
+            passing through each voxel\
+            Options are: sum, min, mean, max (default: mean).
+        backtrack: if no valid timeseries is found at the streamline endpoint,\
+            back-track along the streamline trajectory until a valid timeseries is\
+            found.
+        upsample: upsample the tracks by some ratio using Hermite interpolation\
+            before mapping (if omitted, an appropriate ratio will be determined\
+            automatically).
+        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 `TckdfcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKDFC_METADATA)
+    params = tckdfc_params(
+        static=static,
+        dynamic=dynamic,
+        template=template,
+        vox=vox,
+        stat_vox=stat_vox,
+        backtrack=backtrack,
+        upsample=upsample,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks=tracks,
+        fmri=fmri,
+        output=output,
+    )
+    return tckdfc_execute(params, execution)
+
+
+__all__ = [
+    "TCKDFC_METADATA",
+    "TckdfcConfigParameters",
+    "TckdfcDynamicParameters",
+    "TckdfcOutputs",
+    "TckdfcParameters",
+    "tckdfc",
+    "tckdfc_config_params",
+    "tckdfc_dynamic_params",
+    "tckdfc_params",
+]