niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/dmri_paths.py

@@ -0,0 +1,636 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DMRI_PATHS_METADATA = Metadata(
+    id="6eda0635b358ac171fbbf14d968294d81a352fc1.boutiques",
+    name="dmri_paths",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DmriPathsParameters = typing.TypedDict('DmriPathsParameters', {
+    "__STYX_TYPE__": typing.Literal["dmri_paths"],
+    "indir": typing.NotRequired[str | None],
+    "outdir": typing.NotRequired[str | None],
+    "dwi": typing.NotRequired[InputPathType | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "bval": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bpdir": typing.NotRequired[str | None],
+    "ntr": typing.NotRequired[float | None],
+    "fmin": typing.NotRequired[float | None],
+    "basereg": typing.NotRequired[InputPathType | None],
+    "basemask": typing.NotRequired[InputPathType | None],
+    "roi1": typing.NotRequired[InputPathType | None],
+    "roi2": typing.NotRequired[InputPathType | None],
+    "roimesh1": typing.NotRequired[InputPathType | None],
+    "roimesh2": typing.NotRequired[InputPathType | None],
+    "roiref1": typing.NotRequired[InputPathType | None],
+    "roiref2": typing.NotRequired[InputPathType | None],
+    "prior": typing.NotRequired[InputPathType | None],
+    "nprior": typing.NotRequired[InputPathType | None],
+    "nset": typing.NotRequired[float | None],
+    "lprior": typing.NotRequired[InputPathType | None],
+    "lset": typing.NotRequired[float | None],
+    "seg": typing.NotRequired[InputPathType | None],
+    "tprior": typing.NotRequired[InputPathType | None],
+    "cprior": typing.NotRequired[InputPathType | None],
+    "reg": typing.NotRequired[InputPathType | None],
+    "regnl": typing.NotRequired[InputPathType | None],
+    "init": typing.NotRequired[InputPathType | None],
+    "nb": typing.NotRequired[float | None],
+    "ns": typing.NotRequired[float | None],
+    "nk": typing.NotRequired[float | None],
+    "nu": typing.NotRequired[float | None],
+    "sdp": typing.NotRequired[InputPathType | None],
+    "debug": bool,
+    "checkopts": bool,
+    "version": 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_paths": dmri_paths_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 DmriPathsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dmri_paths(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dmri_paths_params(
+    indir: str | None = None,
+    outdir: str | None = None,
+    dwi: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    bval: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    bpdir: str | None = None,
+    ntr: float | None = 1,
+    fmin: float | None = 0,
+    basereg: InputPathType | None = None,
+    basemask: InputPathType | None = None,
+    roi1: InputPathType | None = None,
+    roi2: InputPathType | None = None,
+    roimesh1: InputPathType | None = None,
+    roimesh2: InputPathType | None = None,
+    roiref1: InputPathType | None = None,
+    roiref2: InputPathType | None = None,
+    prior: InputPathType | None = None,
+    nprior: InputPathType | None = None,
+    nset: float | None = None,
+    lprior: InputPathType | None = None,
+    lset: float | None = None,
+    seg: InputPathType | None = None,
+    tprior: InputPathType | None = None,
+    cprior: InputPathType | None = None,
+    reg: InputPathType | None = None,
+    regnl: InputPathType | None = None,
+    init: InputPathType | None = None,
+    nb: float | None = 5000,
+    ns: float | None = 5000,
+    nk: float | None = 10,
+    nu: float | None = 40,
+    sdp: InputPathType | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+) -> DmriPathsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        indir: Input subject directory (optional), specify multiple for\
+            longitudinal data.
+        outdir: Output directory (one per path).
+        dwi: DWI volume series.
+        grad: Text file of diffusion gradients.
+        bval: Text file of diffusion b-values.
+        mask: Mask volume.
+        bpdir: BEDPOST directory.
+        ntr: Max number of tracts per voxel (default 1).
+        fmin: Tract volume fraction threshold (default 0).
+        basereg: Base-to-DWI registration, needed for longitudinal data only\
+            (.mat, as many as input directories).
+        basemask: Base template mask volume.
+        roi1: End ROI 1 (volume or label, one per path).
+        roi2: End ROI 2 (volume or label, one per path).
+        roimesh1: Mesh for end ROI 1 (for label ROIs).
+        roimesh2: Mesh for end ROI 2 (for label ROIs).
+        roiref1: Reference volume for end ROI 1 (for label ROIs).
+        roiref2: Reference volume for end ROI 2 (for label ROIs).
+        prior: Spatial path priors (negative log-likelihoods off and on the\
+            path, one pair per path).
+        nprior: Near-neighbor label priors (negative log-likelihood and list of\
+            labels, one pair per path).
+        nset: Subset of near-neighbor label priors (default all).
+        lprior: Local-neighbor label priors (negative log-likelihood and list\
+            of labels, one pair per path).
+        lset: Subset of local-neighbor label priors (default all).
+        seg: Segmentation map of test subject, specify multiple for\
+            longitudinal data.
+        tprior: Path tangent vector priors (negative log-likelihood, one per\
+            path).
+        cprior: Path curvature priors (negative log-likelihood, one per path).
+        reg: DWI-to-atlas affine registration (.mat).
+        regnl: DWI-to-atlas nonlinear registration (.m3z).
+        init: Text file of initial control points (one per path).
+        nb: Number of burn-in samples (default 5000).
+        ns: Number of post-burn-in samples (default 5000).
+        nk: Keep every nk-th sample (default 10).
+        nu: Update proposal every nu-th sample (default 40).
+        sdp: Text file with initial proposal standard deviations for control\
+            point perturbations.
+        debug: Turn on debugging.
+        checkopts: Don't run anything, just check options and exit.
+        version: Print out version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dmri_paths",
+        "debug": debug,
+        "checkopts": checkopts,
+        "version": version,
+    }
+    if indir is not None:
+        params["indir"] = indir
+    if outdir is not None:
+        params["outdir"] = outdir
+    if dwi is not None:
+        params["dwi"] = dwi
+    if grad is not None:
+        params["grad"] = grad
+    if bval is not None:
+        params["bval"] = bval
+    if mask is not None:
+        params["mask"] = mask
+    if bpdir is not None:
+        params["bpdir"] = bpdir
+    if ntr is not None:
+        params["ntr"] = ntr
+    if fmin is not None:
+        params["fmin"] = fmin
+    if basereg is not None:
+        params["basereg"] = basereg
+    if basemask is not None:
+        params["basemask"] = basemask
+    if roi1 is not None:
+        params["roi1"] = roi1
+    if roi2 is not None:
+        params["roi2"] = roi2
+    if roimesh1 is not None:
+        params["roimesh1"] = roimesh1
+    if roimesh2 is not None:
+        params["roimesh2"] = roimesh2
+    if roiref1 is not None:
+        params["roiref1"] = roiref1
+    if roiref2 is not None:
+        params["roiref2"] = roiref2
+    if prior is not None:
+        params["prior"] = prior
+    if nprior is not None:
+        params["nprior"] = nprior
+    if nset is not None:
+        params["nset"] = nset
+    if lprior is not None:
+        params["lprior"] = lprior
+    if lset is not None:
+        params["lset"] = lset
+    if seg is not None:
+        params["seg"] = seg
+    if tprior is not None:
+        params["tprior"] = tprior
+    if cprior is not None:
+        params["cprior"] = cprior
+    if reg is not None:
+        params["reg"] = reg
+    if regnl is not None:
+        params["regnl"] = regnl
+    if init is not None:
+        params["init"] = init
+    if nb is not None:
+        params["nb"] = nb
+    if ns is not None:
+        params["ns"] = ns
+    if nk is not None:
+        params["nk"] = nk
+    if nu is not None:
+        params["nu"] = nu
+    if sdp is not None:
+        params["sdp"] = sdp
+    return params
+
+
+def dmri_paths_cargs(
+    params: DmriPathsParameters,
+    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_paths")
+    if params.get("indir") is not None:
+        cargs.extend([
+            "--indir",
+            params.get("indir")
+        ])
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "--outdir",
+            params.get("outdir")
+        ])
+    if params.get("dwi") is not None:
+        cargs.extend([
+            "--dwi",
+            execution.input_file(params.get("dwi"))
+        ])
+    if params.get("grad") is not None:
+        cargs.extend([
+            "--grad",
+            execution.input_file(params.get("grad"))
+        ])
+    if params.get("bval") is not None:
+        cargs.extend([
+            "--bval",
+            execution.input_file(params.get("bval"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bpdir") is not None:
+        cargs.extend([
+            "--bpdir",
+            params.get("bpdir")
+        ])
+    if params.get("ntr") is not None:
+        cargs.extend([
+            "--ntr",
+            str(params.get("ntr"))
+        ])
+    if params.get("fmin") is not None:
+        cargs.extend([
+            "--fmin",
+            str(params.get("fmin"))
+        ])
+    if params.get("basereg") is not None:
+        cargs.extend([
+            "--basereg",
+            execution.input_file(params.get("basereg"))
+        ])
+    if params.get("basemask") is not None:
+        cargs.extend([
+            "--basemask",
+            execution.input_file(params.get("basemask"))
+        ])
+    if params.get("roi1") is not None:
+        cargs.extend([
+            "--roi1",
+            execution.input_file(params.get("roi1"))
+        ])
+    if params.get("roi2") is not None:
+        cargs.extend([
+            "--roi2",
+            execution.input_file(params.get("roi2"))
+        ])
+    if params.get("roimesh1") is not None:
+        cargs.extend([
+            "--roimesh1",
+            execution.input_file(params.get("roimesh1"))
+        ])
+    if params.get("roimesh2") is not None:
+        cargs.extend([
+            "--roimesh2",
+            execution.input_file(params.get("roimesh2"))
+        ])
+    if params.get("roiref1") is not None:
+        cargs.extend([
+            "--roiref1",
+            execution.input_file(params.get("roiref1"))
+        ])
+    if params.get("roiref2") is not None:
+        cargs.extend([
+            "--roiref2",
+            execution.input_file(params.get("roiref2"))
+        ])
+    if params.get("prior") is not None:
+        cargs.extend([
+            "--prior",
+            execution.input_file(params.get("prior"))
+        ])
+    if params.get("nprior") is not None:
+        cargs.extend([
+            "--nprior",
+            execution.input_file(params.get("nprior"))
+        ])
+    if params.get("nset") is not None:
+        cargs.extend([
+            "--nset",
+            str(params.get("nset"))
+        ])
+    if params.get("lprior") is not None:
+        cargs.extend([
+            "--lprior",
+            execution.input_file(params.get("lprior"))
+        ])
+    if params.get("lset") is not None:
+        cargs.extend([
+            "--lset",
+            str(params.get("lset"))
+        ])
+    if params.get("seg") is not None:
+        cargs.extend([
+            "--seg",
+            execution.input_file(params.get("seg"))
+        ])
+    if params.get("tprior") is not None:
+        cargs.extend([
+            "--tprior",
+            execution.input_file(params.get("tprior"))
+        ])
+    if params.get("cprior") is not None:
+        cargs.extend([
+            "--cprior",
+            execution.input_file(params.get("cprior"))
+        ])
+    if params.get("reg") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("reg"))
+        ])
+    if params.get("regnl") is not None:
+        cargs.extend([
+            "--regnl",
+            execution.input_file(params.get("regnl"))
+        ])
+    if params.get("init") is not None:
+        cargs.extend([
+            "--init",
+            execution.input_file(params.get("init"))
+        ])
+    if params.get("nb") is not None:
+        cargs.extend([
+            "--nb",
+            str(params.get("nb"))
+        ])
+    if params.get("ns") is not None:
+        cargs.extend([
+            "--ns",
+            str(params.get("ns"))
+        ])
+    if params.get("nk") is not None:
+        cargs.extend([
+            "--nk",
+            str(params.get("nk"))
+        ])
+    if params.get("nu") is not None:
+        cargs.extend([
+            "--nu",
+            str(params.get("nu"))
+        ])
+    if params.get("sdp") is not None:
+        cargs.extend([
+            "--sdp",
+            execution.input_file(params.get("sdp"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def dmri_paths_outputs(
+    params: DmriPathsParameters,
+    execution: Execution,
+) -> DmriPathsOutputs:
+    """
+    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 = DmriPathsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dmri_paths_execute(
+    params: DmriPathsParameters,
+    execution: Execution,
+) -> DmriPathsOutputs:
+    """
+    Tool for diffusion MRI path analysis.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DmriPathsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dmri_paths_cargs(params, execution)
+    ret = dmri_paths_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dmri_paths(
+    indir: str | None = None,
+    outdir: str | None = None,
+    dwi: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    bval: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    bpdir: str | None = None,
+    ntr: float | None = 1,
+    fmin: float | None = 0,
+    basereg: InputPathType | None = None,
+    basemask: InputPathType | None = None,
+    roi1: InputPathType | None = None,
+    roi2: InputPathType | None = None,
+    roimesh1: InputPathType | None = None,
+    roimesh2: InputPathType | None = None,
+    roiref1: InputPathType | None = None,
+    roiref2: InputPathType | None = None,
+    prior: InputPathType | None = None,
+    nprior: InputPathType | None = None,
+    nset: float | None = None,
+    lprior: InputPathType | None = None,
+    lset: float | None = None,
+    seg: InputPathType | None = None,
+    tprior: InputPathType | None = None,
+    cprior: InputPathType | None = None,
+    reg: InputPathType | None = None,
+    regnl: InputPathType | None = None,
+    init: InputPathType | None = None,
+    nb: float | None = 5000,
+    ns: float | None = 5000,
+    nk: float | None = 10,
+    nu: float | None = 40,
+    sdp: InputPathType | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DmriPathsOutputs:
+    """
+    Tool for diffusion MRI path analysis.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        indir: Input subject directory (optional), specify multiple for\
+            longitudinal data.
+        outdir: Output directory (one per path).
+        dwi: DWI volume series.
+        grad: Text file of diffusion gradients.
+        bval: Text file of diffusion b-values.
+        mask: Mask volume.
+        bpdir: BEDPOST directory.
+        ntr: Max number of tracts per voxel (default 1).
+        fmin: Tract volume fraction threshold (default 0).
+        basereg: Base-to-DWI registration, needed for longitudinal data only\
+            (.mat, as many as input directories).
+        basemask: Base template mask volume.
+        roi1: End ROI 1 (volume or label, one per path).
+        roi2: End ROI 2 (volume or label, one per path).
+        roimesh1: Mesh for end ROI 1 (for label ROIs).
+        roimesh2: Mesh for end ROI 2 (for label ROIs).
+        roiref1: Reference volume for end ROI 1 (for label ROIs).
+        roiref2: Reference volume for end ROI 2 (for label ROIs).
+        prior: Spatial path priors (negative log-likelihoods off and on the\
+            path, one pair per path).
+        nprior: Near-neighbor label priors (negative log-likelihood and list of\
+            labels, one pair per path).
+        nset: Subset of near-neighbor label priors (default all).
+        lprior: Local-neighbor label priors (negative log-likelihood and list\
+            of labels, one pair per path).
+        lset: Subset of local-neighbor label priors (default all).
+        seg: Segmentation map of test subject, specify multiple for\
+            longitudinal data.
+        tprior: Path tangent vector priors (negative log-likelihood, one per\
+            path).
+        cprior: Path curvature priors (negative log-likelihood, one per path).
+        reg: DWI-to-atlas affine registration (.mat).
+        regnl: DWI-to-atlas nonlinear registration (.m3z).
+        init: Text file of initial control points (one per path).
+        nb: Number of burn-in samples (default 5000).
+        ns: Number of post-burn-in samples (default 5000).
+        nk: Keep every nk-th sample (default 10).
+        nu: Update proposal every nu-th sample (default 40).
+        sdp: Text file with initial proposal standard deviations for control\
+            point perturbations.
+        debug: Turn on debugging.
+        checkopts: Don't run anything, just check options and exit.
+        version: Print out version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DmriPathsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_PATHS_METADATA)
+    params = dmri_paths_params(
+        indir=indir,
+        outdir=outdir,
+        dwi=dwi,
+        grad=grad,
+        bval=bval,
+        mask=mask,
+        bpdir=bpdir,
+        ntr=ntr,
+        fmin=fmin,
+        basereg=basereg,
+        basemask=basemask,
+        roi1=roi1,
+        roi2=roi2,
+        roimesh1=roimesh1,
+        roimesh2=roimesh2,
+        roiref1=roiref1,
+        roiref2=roiref2,
+        prior=prior,
+        nprior=nprior,
+        nset=nset,
+        lprior=lprior,
+        lset=lset,
+        seg=seg,
+        tprior=tprior,
+        cprior=cprior,
+        reg=reg,
+        regnl=regnl,
+        init=init,
+        nb=nb,
+        ns=ns,
+        nk=nk,
+        nu=nu,
+        sdp=sdp,
+        debug=debug,
+        checkopts=checkopts,
+        version=version,
+    )
+    return dmri_paths_execute(params, execution)
+
+
+__all__ = [
+    "DMRI_PATHS_METADATA",
+    "DmriPathsOutputs",
+    "DmriPathsParameters",
+    "dmri_paths",
+    "dmri_paths_params",
+]