niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/dmri_trk2trk.py

@@ -0,0 +1,507 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DMRI_TRK2TRK_METADATA = Metadata(
+    id="7065b499ec2cb8133b9197d9f36d138deaee55a7.boutiques",
+    name="dmri_trk2trk",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DmriTrk2trkParameters = typing.TypedDict('DmriTrk2trkParameters', {
+    "__STYX_TYPE__": typing.Literal["dmri_trk2trk"],
+    "in_trk": list[InputPathType],
+    "in_asc": typing.NotRequired[list[InputPathType] | None],
+    "in_dir": typing.NotRequired[str | None],
+    "out_trk": typing.NotRequired[str | None],
+    "out_asc": typing.NotRequired[str | None],
+    "out_vol": typing.NotRequired[str | None],
+    "out_dir": typing.NotRequired[str | None],
+    "in_ref": typing.NotRequired[InputPathType | None],
+    "out_ref": typing.NotRequired[InputPathType | None],
+    "reg_file": typing.NotRequired[InputPathType | None],
+    "regnl_file": typing.NotRequired[InputPathType | None],
+    "inv_flag": bool,
+    "fill_flag": bool,
+    "overlay": typing.NotRequired[list[InputPathType] | None],
+    "inclusion_mask": typing.NotRequired[list[InputPathType] | None],
+    "exclusion_mask": typing.NotRequired[list[InputPathType] | None],
+    "terminal_inclusion_mask": typing.NotRequired[list[InputPathType] | None],
+    "terminal_exclusion_mask": typing.NotRequired[list[InputPathType] | None],
+    "length_min": typing.NotRequired[float | None],
+    "length_max": typing.NotRequired[float | None],
+    "mean_flag": bool,
+    "nearmean_flag": bool,
+    "nth_streamline": typing.NotRequired[float | None],
+    "every_nth_streamline": typing.NotRequired[float | None],
+    "smooth_flag": bool,
+    "debug_flag": bool,
+    "check_opts": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dmri_trk2trk": dmri_trk2trk_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 {
+        "dmri_trk2trk": dmri_trk2trk_outputs,
+    }.get(t)
+
+
+class DmriTrk2trkOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dmri_trk2trk(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_trk_file: OutputPathType | None
+    """Transformed output .trk file"""
+    out_asc_file: OutputPathType | None
+    """Transformed output ASCII text file"""
+    out_vol_file: OutputPathType | None
+    """Transformed output volume"""
+
+
+def dmri_trk2trk_params(
+    in_trk: list[InputPathType],
+    in_asc: list[InputPathType] | None = None,
+    in_dir: str | None = None,
+    out_trk: str | None = None,
+    out_asc: str | None = None,
+    out_vol: str | None = None,
+    out_dir: str | None = None,
+    in_ref: InputPathType | None = None,
+    out_ref: InputPathType | None = None,
+    reg_file: InputPathType | None = None,
+    regnl_file: InputPathType | None = None,
+    inv_flag: bool = False,
+    fill_flag: bool = False,
+    overlay: list[InputPathType] | None = None,
+    inclusion_mask: list[InputPathType] | None = None,
+    exclusion_mask: list[InputPathType] | None = None,
+    terminal_inclusion_mask: list[InputPathType] | None = None,
+    terminal_exclusion_mask: list[InputPathType] | None = None,
+    length_min: float | None = None,
+    length_max: float | None = None,
+    mean_flag: bool = False,
+    nearmean_flag: bool = False,
+    nth_streamline: float | None = None,
+    every_nth_streamline: float | None = None,
+    smooth_flag: bool = False,
+    debug_flag: bool = False,
+    check_opts: bool = False,
+) -> DmriTrk2trkParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_trk: Input .trk file(s).
+        in_asc: Input ASCII plain text file(s), as an alternative to .trk.
+        in_dir: Input directory (optional).
+        out_trk: Output .trk file(s), as many as inputs (or 1 to merge inputs).
+        out_asc: Output ASCII plain text file(s), as many as inputs (or 1 to\
+            merge inputs).
+        out_vol: Output volume(s), as many as inputs (or 1 to merge inputs).
+        out_dir: Output directory (optional).
+        in_ref: Input reference volume (needed for --reg/--regnl).
+        out_ref: Output reference volume (needed for --reg/--regnl/--outvol).
+        reg_file: Affine registration file (.lta or .mat), applied first.
+        regnl_file: Nonlinear registration file (.m3z), applied second.
+        inv_flag: Apply inverse of registration (default: no).
+        fill_flag: Fill gaps b/w mapped points by linear interpolation.
+        overlay: Scalar overlay 1D volume(s), applied to all input .trk files.
+        inclusion_mask: Inclusion mask(s), applied to all input .trk files.
+        exclusion_mask: Exclusion mask(s), applied to all input .trk files.
+        terminal_inclusion_mask: Terminal inclusion mask(s), applied to all\
+            input .trk files.
+        terminal_exclusion_mask: Terminal exclusion mask(s), applied to all\
+            input .trk files.
+        length_min: Only save streamlines with length greater than this number.
+        length_max: Only save streamlines with length smaller than this number.
+        mean_flag: Only save the mean of the streamlines (Default: save all).
+        nearmean_flag: Only save the streamline nearest to the mean (Default:\
+            save all).
+        nth_streamline: Only save the n-th (0-based) streamline (Default: save\
+            all).
+        every_nth_streamline: Only save every n-th streamline (Default: save\
+            all).
+        smooth_flag: Smooth streamlines (default: no).
+        debug_flag: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dmri_trk2trk",
+        "in_trk": in_trk,
+        "inv_flag": inv_flag,
+        "fill_flag": fill_flag,
+        "mean_flag": mean_flag,
+        "nearmean_flag": nearmean_flag,
+        "smooth_flag": smooth_flag,
+        "debug_flag": debug_flag,
+        "check_opts": check_opts,
+    }
+    if in_asc is not None:
+        params["in_asc"] = in_asc
+    if in_dir is not None:
+        params["in_dir"] = in_dir
+    if out_trk is not None:
+        params["out_trk"] = out_trk
+    if out_asc is not None:
+        params["out_asc"] = out_asc
+    if out_vol is not None:
+        params["out_vol"] = out_vol
+    if out_dir is not None:
+        params["out_dir"] = out_dir
+    if in_ref is not None:
+        params["in_ref"] = in_ref
+    if out_ref is not None:
+        params["out_ref"] = out_ref
+    if reg_file is not None:
+        params["reg_file"] = reg_file
+    if regnl_file is not None:
+        params["regnl_file"] = regnl_file
+    if overlay is not None:
+        params["overlay"] = overlay
+    if inclusion_mask is not None:
+        params["inclusion_mask"] = inclusion_mask
+    if exclusion_mask is not None:
+        params["exclusion_mask"] = exclusion_mask
+    if terminal_inclusion_mask is not None:
+        params["terminal_inclusion_mask"] = terminal_inclusion_mask
+    if terminal_exclusion_mask is not None:
+        params["terminal_exclusion_mask"] = terminal_exclusion_mask
+    if length_min is not None:
+        params["length_min"] = length_min
+    if length_max is not None:
+        params["length_max"] = length_max
+    if nth_streamline is not None:
+        params["nth_streamline"] = nth_streamline
+    if every_nth_streamline is not None:
+        params["every_nth_streamline"] = every_nth_streamline
+    return params
+
+
+def dmri_trk2trk_cargs(
+    params: DmriTrk2trkParameters,
+    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("dmri_trk2trk")
+    cargs.extend([
+        "--in",
+        *[execution.input_file(f) for f in params.get("in_trk")]
+    ])
+    if params.get("in_asc") is not None:
+        cargs.extend([
+            "--inasc",
+            *[execution.input_file(f) for f in params.get("in_asc")]
+        ])
+    if params.get("in_dir") is not None:
+        cargs.extend([
+            "--indir",
+            params.get("in_dir")
+        ])
+    if params.get("out_trk") is not None:
+        cargs.extend([
+            "--out",
+            params.get("out_trk")
+        ])
+    if params.get("out_asc") is not None:
+        cargs.extend([
+            "--outasc",
+            params.get("out_asc")
+        ])
+    if params.get("out_vol") is not None:
+        cargs.extend([
+            "--outvol",
+            params.get("out_vol")
+        ])
+    if params.get("out_dir") is not None:
+        cargs.extend([
+            "--outdir",
+            params.get("out_dir")
+        ])
+    if params.get("in_ref") is not None:
+        cargs.extend([
+            "--inref",
+            execution.input_file(params.get("in_ref"))
+        ])
+    if params.get("out_ref") is not None:
+        cargs.extend([
+            "--outref",
+            execution.input_file(params.get("out_ref"))
+        ])
+    if params.get("reg_file") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("reg_file"))
+        ])
+    if params.get("regnl_file") is not None:
+        cargs.extend([
+            "--regnl",
+            execution.input_file(params.get("regnl_file"))
+        ])
+    if params.get("inv_flag"):
+        cargs.append("--inv")
+    if params.get("fill_flag"):
+        cargs.append("--fill")
+    if params.get("overlay") is not None:
+        cargs.extend([
+            "--over",
+            *[execution.input_file(f) for f in params.get("overlay")]
+        ])
+    if params.get("inclusion_mask") is not None:
+        cargs.extend([
+            "--imask",
+            *[execution.input_file(f) for f in params.get("inclusion_mask")]
+        ])
+    if params.get("exclusion_mask") is not None:
+        cargs.extend([
+            "--emask",
+            *[execution.input_file(f) for f in params.get("exclusion_mask")]
+        ])
+    if params.get("terminal_inclusion_mask") is not None:
+        cargs.extend([
+            "--itmask",
+            *[execution.input_file(f) for f in params.get("terminal_inclusion_mask")]
+        ])
+    if params.get("terminal_exclusion_mask") is not None:
+        cargs.extend([
+            "--etmask",
+            *[execution.input_file(f) for f in params.get("terminal_exclusion_mask")]
+        ])
+    if params.get("length_min") is not None:
+        cargs.extend([
+            "--lmin",
+            str(params.get("length_min"))
+        ])
+    if params.get("length_max") is not None:
+        cargs.extend([
+            "--lmax",
+            str(params.get("length_max"))
+        ])
+    if params.get("mean_flag"):
+        cargs.append("--mean")
+    if params.get("nearmean_flag"):
+        cargs.append("--nearmean")
+    if params.get("nth_streamline") is not None:
+        cargs.extend([
+            "--nth",
+            str(params.get("nth_streamline"))
+        ])
+    if params.get("every_nth_streamline") is not None:
+        cargs.extend([
+            "--every",
+            str(params.get("every_nth_streamline"))
+        ])
+    if params.get("smooth_flag"):
+        cargs.append("--smooth")
+    if params.get("debug_flag"):
+        cargs.append("--debug")
+    if params.get("check_opts"):
+        cargs.append("--checkopts")
+    return cargs
+
+
+def dmri_trk2trk_outputs(
+    params: DmriTrk2trkParameters,
+    execution: Execution,
+) -> DmriTrk2trkOutputs:
+    """
+    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 = DmriTrk2trkOutputs(
+        root=execution.output_file("."),
+        out_trk_file=execution.output_file(params.get("out_trk")) if (params.get("out_trk") is not None) else None,
+        out_asc_file=execution.output_file(params.get("out_asc")) if (params.get("out_asc") is not None) else None,
+        out_vol_file=execution.output_file(params.get("out_vol")) if (params.get("out_vol") is not None) else None,
+    )
+    return ret
+
+
+def dmri_trk2trk_execute(
+    params: DmriTrk2trkParameters,
+    execution: Execution,
+) -> DmriTrk2trkOutputs:
+    """
+    A tool for transforming and analyzing tractography data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DmriTrk2trkOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dmri_trk2trk_cargs(params, execution)
+    ret = dmri_trk2trk_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dmri_trk2trk(
+    in_trk: list[InputPathType],
+    in_asc: list[InputPathType] | None = None,
+    in_dir: str | None = None,
+    out_trk: str | None = None,
+    out_asc: str | None = None,
+    out_vol: str | None = None,
+    out_dir: str | None = None,
+    in_ref: InputPathType | None = None,
+    out_ref: InputPathType | None = None,
+    reg_file: InputPathType | None = None,
+    regnl_file: InputPathType | None = None,
+    inv_flag: bool = False,
+    fill_flag: bool = False,
+    overlay: list[InputPathType] | None = None,
+    inclusion_mask: list[InputPathType] | None = None,
+    exclusion_mask: list[InputPathType] | None = None,
+    terminal_inclusion_mask: list[InputPathType] | None = None,
+    terminal_exclusion_mask: list[InputPathType] | None = None,
+    length_min: float | None = None,
+    length_max: float | None = None,
+    mean_flag: bool = False,
+    nearmean_flag: bool = False,
+    nth_streamline: float | None = None,
+    every_nth_streamline: float | None = None,
+    smooth_flag: bool = False,
+    debug_flag: bool = False,
+    check_opts: bool = False,
+    runner: Runner | None = None,
+) -> DmriTrk2trkOutputs:
+    """
+    A tool for transforming and analyzing tractography data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        in_trk: Input .trk file(s).
+        in_asc: Input ASCII plain text file(s), as an alternative to .trk.
+        in_dir: Input directory (optional).
+        out_trk: Output .trk file(s), as many as inputs (or 1 to merge inputs).
+        out_asc: Output ASCII plain text file(s), as many as inputs (or 1 to\
+            merge inputs).
+        out_vol: Output volume(s), as many as inputs (or 1 to merge inputs).
+        out_dir: Output directory (optional).
+        in_ref: Input reference volume (needed for --reg/--regnl).
+        out_ref: Output reference volume (needed for --reg/--regnl/--outvol).
+        reg_file: Affine registration file (.lta or .mat), applied first.
+        regnl_file: Nonlinear registration file (.m3z), applied second.
+        inv_flag: Apply inverse of registration (default: no).
+        fill_flag: Fill gaps b/w mapped points by linear interpolation.
+        overlay: Scalar overlay 1D volume(s), applied to all input .trk files.
+        inclusion_mask: Inclusion mask(s), applied to all input .trk files.
+        exclusion_mask: Exclusion mask(s), applied to all input .trk files.
+        terminal_inclusion_mask: Terminal inclusion mask(s), applied to all\
+            input .trk files.
+        terminal_exclusion_mask: Terminal exclusion mask(s), applied to all\
+            input .trk files.
+        length_min: Only save streamlines with length greater than this number.
+        length_max: Only save streamlines with length smaller than this number.
+        mean_flag: Only save the mean of the streamlines (Default: save all).
+        nearmean_flag: Only save the streamline nearest to the mean (Default:\
+            save all).
+        nth_streamline: Only save the n-th (0-based) streamline (Default: save\
+            all).
+        every_nth_streamline: Only save every n-th streamline (Default: save\
+            all).
+        smooth_flag: Smooth streamlines (default: no).
+        debug_flag: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DmriTrk2trkOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_TRK2TRK_METADATA)
+    params = dmri_trk2trk_params(
+        in_trk=in_trk,
+        in_asc=in_asc,
+        in_dir=in_dir,
+        out_trk=out_trk,
+        out_asc=out_asc,
+        out_vol=out_vol,
+        out_dir=out_dir,
+        in_ref=in_ref,
+        out_ref=out_ref,
+        reg_file=reg_file,
+        regnl_file=regnl_file,
+        inv_flag=inv_flag,
+        fill_flag=fill_flag,
+        overlay=overlay,
+        inclusion_mask=inclusion_mask,
+        exclusion_mask=exclusion_mask,
+        terminal_inclusion_mask=terminal_inclusion_mask,
+        terminal_exclusion_mask=terminal_exclusion_mask,
+        length_min=length_min,
+        length_max=length_max,
+        mean_flag=mean_flag,
+        nearmean_flag=nearmean_flag,
+        nth_streamline=nth_streamline,
+        every_nth_streamline=every_nth_streamline,
+        smooth_flag=smooth_flag,
+        debug_flag=debug_flag,
+        check_opts=check_opts,
+    )
+    return dmri_trk2trk_execute(params, execution)
+
+
+__all__ = [
+    "DMRI_TRK2TRK_METADATA",
+    "DmriTrk2trkOutputs",
+    "DmriTrk2trkParameters",
+    "dmri_trk2trk",
+    "dmri_trk2trk_params",
+]

niwrap_freesurfer/freesurfer/dmri_violin_plots.py

@@ -0,0 +1,197 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DMRI_VIOLIN_PLOTS_METADATA = Metadata(
+    id="a193f3c5d1fcce153b59c31f2df32aafdf44cb45.boutiques",
+    name="dmri_violinPlots",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DmriViolinPlotsParameters = typing.TypedDict('DmriViolinPlotsParameters', {
+    "__STYX_TYPE__": typing.Literal["dmri_violinPlots"],
+    "input_directory": str,
+    "labels": InputPathType,
+    "structure": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dmri_violinPlots": dmri_violin_plots_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 {
+    }.get(t)
+
+
+class DmriViolinPlotsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dmri_violin_plots(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dmri_violin_plots_params(
+    input_directory: str,
+    labels: InputPathType,
+    structure: str,
+) -> DmriViolinPlotsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_directory: Directory with all subjects.
+        labels: CSV file with group labels.
+        structure: Name of the structure.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dmri_violinPlots",
+        "input_directory": input_directory,
+        "labels": labels,
+        "structure": structure,
+    }
+    return params
+
+
+def dmri_violin_plots_cargs(
+    params: DmriViolinPlotsParameters,
+    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("dmri_violinPlots")
+    cargs.extend([
+        "-i",
+        params.get("input_directory")
+    ])
+    cargs.extend([
+        "-l",
+        execution.input_file(params.get("labels"))
+    ])
+    cargs.extend([
+        "-s",
+        params.get("structure")
+    ])
+    return cargs
+
+
+def dmri_violin_plots_outputs(
+    params: DmriViolinPlotsParameters,
+    execution: Execution,
+) -> DmriViolinPlotsOutputs:
+    """
+    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 = DmriViolinPlotsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dmri_violin_plots_execute(
+    params: DmriViolinPlotsParameters,
+    execution: Execution,
+) -> DmriViolinPlotsOutputs:
+    """
+    Generate violin plots for dMRI data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DmriViolinPlotsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dmri_violin_plots_cargs(params, execution)
+    ret = dmri_violin_plots_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dmri_violin_plots(
+    input_directory: str,
+    labels: InputPathType,
+    structure: str,
+    runner: Runner | None = None,
+) -> DmriViolinPlotsOutputs:
+    """
+    Generate violin plots for dMRI data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_directory: Directory with all subjects.
+        labels: CSV file with group labels.
+        structure: Name of the structure.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DmriViolinPlotsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_VIOLIN_PLOTS_METADATA)
+    params = dmri_violin_plots_params(
+        input_directory=input_directory,
+        labels=labels,
+        structure=structure,
+    )
+    return dmri_violin_plots_execute(params, execution)
+
+
+__all__ = [
+    "DMRI_VIOLIN_PLOTS_METADATA",
+    "DmriViolinPlotsOutputs",
+    "DmriViolinPlotsParameters",
+    "dmri_violin_plots",
+    "dmri_violin_plots_params",
+]