niwrap-afni 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_afni/afni/v_3d_dtto_dwi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DTTO_DWI_METADATA = Metadata(
-    id="0f0fbb0dc2b7d522416ef673b66be8d6a5895cef.boutiques",
+    id="3ce4d55f82946de86dac4267e097694ede4e7771.boutiques",
     name="3dDTtoDWI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,6 +18,11 @@ V3dDttoDwiParameters = typing.TypedDict('V3dDttoDwiParameters', {
     "gradient_file": InputPathType,
     "i0_dataset": InputPathType,
     "dt_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "datum_type": typing.NotRequired[str | None],
+    "scale_out_1000": bool,
+    "help": bool,
 })
 
 
@@ -59,7 +64,7 @@ class V3dDttoDwiOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_dwi: OutputPathType
+    output_dwi: OutputPathType | None
     """Computed DWI images including sub-brick for each gradient vector."""
 
 
@@ -67,6 +72,11 @@ def v_3d_dtto_dwi_params(
     gradient_file: InputPathType,
     i0_dataset: InputPathType,
     dt_dataset: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    datum_type: str | None = None,
+    scale_out_1000: bool = False,
+    help_: bool = False,
 ) -> V3dDttoDwiParameters:
     """
     Build parameters.
@@ -77,6 +87,12 @@ def v_3d_dtto_dwi_params(
         i0_dataset: Volume without any gradient applied.
         dt_dataset: 6-sub-brick dataset containing the diffusion tensor data\
             (Dxx, Dxy, Dyy, Dxz, Dyz, Dzz).
+        prefix: Prefix for the output dataset name.
+        automask: Compute gradient images only for high-intensity (brain)\
+            voxels.
+        datum_type: Type of the output dataset (float, short, or byte).
+        scale_out_1000: Match with 3dDWItoDT's '-scale_out_1000' functionality.
+        help_: Show help message.
     Returns:
         Parameter dictionary
     """
@@ -85,7 +101,14 @@ def v_3d_dtto_dwi_params(
         "gradient_file": gradient_file,
         "i0_dataset": i0_dataset,
         "dt_dataset": dt_dataset,
+        "automask": automask,
+        "scale_out_1000": scale_out_1000,
+        "help": help_,
     }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum_type is not None:
+        params["datum_type"] = datum_type
     return params
 
 
@@ -104,10 +127,25 @@ def v_3d_dtto_dwi_cargs(
     """
     cargs = []
     cargs.append("3dDTtoDWI")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("gradient_file")))
     cargs.append(execution.input_file(params.get("i0_dataset")))
     cargs.append(execution.input_file(params.get("dt_dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("datum_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum_type")
+        ])
+    if params.get("scale_out_1000"):
+        cargs.append("-scale_out_1000")
+    if params.get("help"):
+        cargs.append("-help")
     return cargs
 
 
@@ -126,7 +164,7 @@ def v_3d_dtto_dwi_outputs(
     """
     ret = V3dDttoDwiOutputs(
         root=execution.output_file("."),
-        output_dwi=execution.output_file("[PREFIX]*.HEAD"),
+        output_dwi=execution.output_file(params.get("prefix") + "*.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
@@ -160,6 +198,11 @@ def v_3d_dtto_dwi(
     gradient_file: InputPathType,
     i0_dataset: InputPathType,
     dt_dataset: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    datum_type: str | None = None,
+    scale_out_1000: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> V3dDttoDwiOutputs:
     """
@@ -176,6 +219,12 @@ def v_3d_dtto_dwi(
         i0_dataset: Volume without any gradient applied.
         dt_dataset: 6-sub-brick dataset containing the diffusion tensor data\
             (Dxx, Dxy, Dyy, Dxz, Dyz, Dzz).
+        prefix: Prefix for the output dataset name.
+        automask: Compute gradient images only for high-intensity (brain)\
+            voxels.
+        datum_type: Type of the output dataset (float, short, or byte).
+        scale_out_1000: Match with 3dDWItoDT's '-scale_out_1000' functionality.
+        help_: Show help message.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDttoDwiOutputs`).
@@ -186,6 +235,11 @@ def v_3d_dtto_dwi(
         gradient_file=gradient_file,
         i0_dataset=i0_dataset,
         dt_dataset=dt_dataset,
+        prefix=prefix,
+        automask=automask,
+        datum_type=datum_type,
+        scale_out_1000=scale_out_1000,
+        help_=help_,
     )
     return v_3d_dtto_dwi_execute(params, execution)
 

niwrap_afni/afni/v_3d_dwito_dt.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DWITO_DT_METADATA = Metadata(
-    id="edef0edb2012159a76d51a09912a5bd6c5660ab2.boutiques",
+    id="09d06c55d013b2bd12bb78a05cda82297b034024.boutiques",
     name="3dDWItoDT",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,30 @@ V3dDwitoDtParameters = typing.TypedDict('V3dDwitoDtParameters', {
     "__STYX_TYPE__": typing.Literal["3dDWItoDT"],
     "gradient_file": InputPathType,
     "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "bmatrix_NZ": typing.NotRequired[InputPathType | None],
+    "bmatrix_Z": typing.NotRequired[InputPathType | None],
+    "bmatrix_FULL": typing.NotRequired[InputPathType | None],
+    "scale_out_1000": bool,
+    "bmax_ref": typing.NotRequired[float | None],
+    "nonlinear": bool,
+    "linear": bool,
+    "reweight": bool,
+    "max_iter": typing.NotRequired[int | None],
+    "max_iter_rw": typing.NotRequired[int | None],
+    "eigs": bool,
+    "debug_briks": bool,
+    "cumulative_wts": bool,
+    "verbose": typing.NotRequired[int | None],
+    "drive_afni": typing.NotRequired[int | None],
+    "sep_dsets": bool,
+    "csf_val": typing.NotRequired[float | None],
+    "min_bad_md": typing.NotRequired[int | None],
+    "csf_fa": typing.NotRequired[float | None],
+    "opt": typing.NotRequired[str | None],
+    "mean_b0": bool,
 })
 
 
@@ -65,6 +89,30 @@ class V3dDwitoDtOutputs(typing.NamedTuple):
 def v_3d_dwito_dt_params(
     gradient_file: InputPathType,
     dataset: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    bmatrix_nz: InputPathType | None = None,
+    bmatrix_z: InputPathType | None = None,
+    bmatrix_full: InputPathType | None = None,
+    scale_out_1000: bool = False,
+    bmax_ref: float | None = None,
+    nonlinear: bool = False,
+    linear: bool = False,
+    reweight: bool = False,
+    max_iter: int | None = None,
+    max_iter_rw: int | None = None,
+    eigs: bool = False,
+    debug_briks: bool = False,
+    cumulative_wts: bool = False,
+    verbose: int | None = None,
+    drive_afni: int | None = None,
+    sep_dsets: bool = False,
+    csf_val: float | None = None,
+    min_bad_md: int | None = None,
+    csf_fa: float | None = None,
+    opt: str | None = None,
+    mean_b0: bool = False,
 ) -> V3dDwitoDtParameters:
     """
     Build parameters.
@@ -74,6 +122,43 @@ def v_3d_dwito_dt_params(
             floats (Gxi, Gyi, Gzi) or a 1D file of b-matrix elements.
         dataset: A 3D bucket dataset with Np+1 sub-briks where the first\
             sub-brik is the volume acquired with no diffusion weighting.
+        prefix: Output dataset prefix name. Default is 'DT'.
+        automask: Mask dataset so that tensors are computed only for\
+            high-intensity (presumably brain) voxels.
+        mask: Use this dataset as mask to include/exclude voxels.
+        bmatrix_nz: Input dataset is b-matrix, not gradient directions, and\
+            there is no row of zeros at the top of the file.
+        bmatrix_z: Similar to '-bmatrix_NZ' but first row of the file is all\
+            zeros.
+        bmatrix_full: Same as '-bmatrix_Z' but with a more intuitive name.
+        scale_out_1000: Increase output parameters with physical units by\
+            multiplying them by 1000.
+        bmax_ref: Flag the reference b-value if it is greater than zero.
+        nonlinear: Compute iterative solution to avoid negative eigenvalues.\
+            This is the default method.
+        linear: Compute simple linear solution.
+        reweight: Recompute weight factors at end of iterations and restart.
+        max_iter: Maximum number of iterations for convergence. Default is 10.
+        max_iter_rw: Max number of iterations after reweighting. Default is 5.
+        eigs: Compute eigenvalues, eigenvectors, fractional anisotropy, and\
+            mean diffusivity in sub-briks 6-19.
+        debug_briks: Add sub-briks with error functional, original error,\
+            number of steps to convergence, and modeled B0 volume.
+        cumulative_wts: Show overall weight factors for each gradient level.
+        verbose: Print convergence steps every nnnnn voxels.
+        drive_afni: Show convergence graphs every nnnnn voxels. AFNI must have\
+            NIML communications on.
+        sep_dsets: Save tensor, eigenvalues, vectors, FA, MD in separate\
+            datasets.
+        csf_val: Assign diffusivity value to DWI data where the mean values for\
+            b=0 volumes is less than the mean of the remaining volumes at each\
+            voxel.
+        min_bad_md: Change the min MD value used as a 'badness check' for\
+            tensor fits.
+        csf_fa: Assign a specific FA value to CSF voxels.
+        opt: Optimization method: 'powell', 'gradient', or 'hybrid'.
+        mean_b0: Use mean of all b=0 volumes for linear computation and initial\
+            linear for nonlinear method.
     Returns:
         Parameter dictionary
     """
@@ -81,7 +166,45 @@ def v_3d_dwito_dt_params(
         "__STYXTYPE__": "3dDWItoDT",
         "gradient_file": gradient_file,
         "dataset": dataset,
+        "automask": automask,
+        "scale_out_1000": scale_out_1000,
+        "nonlinear": nonlinear,
+        "linear": linear,
+        "reweight": reweight,
+        "eigs": eigs,
+        "debug_briks": debug_briks,
+        "cumulative_wts": cumulative_wts,
+        "sep_dsets": sep_dsets,
+        "mean_b0": mean_b0,
     }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if mask is not None:
+        params["mask"] = mask
+    if bmatrix_nz is not None:
+        params["bmatrix_NZ"] = bmatrix_nz
+    if bmatrix_z is not None:
+        params["bmatrix_Z"] = bmatrix_z
+    if bmatrix_full is not None:
+        params["bmatrix_FULL"] = bmatrix_full
+    if bmax_ref is not None:
+        params["bmax_ref"] = bmax_ref
+    if max_iter is not None:
+        params["max_iter"] = max_iter
+    if max_iter_rw is not None:
+        params["max_iter_rw"] = max_iter_rw
+    if verbose is not None:
+        params["verbose"] = verbose
+    if drive_afni is not None:
+        params["drive_afni"] = drive_afni
+    if csf_val is not None:
+        params["csf_val"] = csf_val
+    if min_bad_md is not None:
+        params["min_bad_md"] = min_bad_md
+    if csf_fa is not None:
+        params["csf_fa"] = csf_fa
+    if opt is not None:
+        params["opt"] = opt
     return params
 
 
@@ -100,9 +223,98 @@ def v_3d_dwito_dt_cargs(
     """
     cargs = []
     cargs.append("3dDWItoDT")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("gradient_file")))
     cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bmatrix_NZ") is not None:
+        cargs.extend([
+            "-bmatrix_NZ",
+            execution.input_file(params.get("bmatrix_NZ"))
+        ])
+    if params.get("bmatrix_Z") is not None:
+        cargs.extend([
+            "-bmatrix_Z",
+            execution.input_file(params.get("bmatrix_Z"))
+        ])
+    if params.get("bmatrix_FULL") is not None:
+        cargs.extend([
+            "-bmatrix_FULL",
+            execution.input_file(params.get("bmatrix_FULL"))
+        ])
+    if params.get("scale_out_1000"):
+        cargs.append("-scale_out_1000")
+    if params.get("bmax_ref") is not None:
+        cargs.extend([
+            "-bmax_ref",
+            str(params.get("bmax_ref"))
+        ])
+    if params.get("nonlinear"):
+        cargs.append("-nonlinear")
+    if params.get("linear"):
+        cargs.append("-linear")
+    if params.get("reweight"):
+        cargs.append("-reweight")
+    if params.get("max_iter") is not None:
+        cargs.extend([
+            "-max_iter",
+            str(params.get("max_iter"))
+        ])
+    if params.get("max_iter_rw") is not None:
+        cargs.extend([
+            "-max_iter_rw",
+            str(params.get("max_iter_rw"))
+        ])
+    if params.get("eigs"):
+        cargs.append("-eigs")
+    if params.get("debug_briks"):
+        cargs.append("-debug_briks")
+    if params.get("cumulative_wts"):
+        cargs.append("-cumulative_wts")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verbose",
+            str(params.get("verbose"))
+        ])
+    if params.get("drive_afni") is not None:
+        cargs.extend([
+            "-drive_afni",
+            str(params.get("drive_afni"))
+        ])
+    if params.get("sep_dsets"):
+        cargs.append("-sep_dsets")
+    if params.get("csf_val") is not None:
+        cargs.extend([
+            "-csf_val",
+            str(params.get("csf_val"))
+        ])
+    if params.get("min_bad_md") is not None:
+        cargs.extend([
+            "-min_bad_md",
+            str(params.get("min_bad_md"))
+        ])
+    if params.get("csf_fa") is not None:
+        cargs.extend([
+            "-csf_fa",
+            str(params.get("csf_fa"))
+        ])
+    if params.get("opt") is not None:
+        cargs.extend([
+            "-opt",
+            params.get("opt")
+        ])
+    if params.get("mean_b0"):
+        cargs.append("-mean_b0")
     return cargs
 
 
@@ -154,6 +366,30 @@ def v_3d_dwito_dt_execute(
 def v_3d_dwito_dt(
     gradient_file: InputPathType,
     dataset: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    bmatrix_nz: InputPathType | None = None,
+    bmatrix_z: InputPathType | None = None,
+    bmatrix_full: InputPathType | None = None,
+    scale_out_1000: bool = False,
+    bmax_ref: float | None = None,
+    nonlinear: bool = False,
+    linear: bool = False,
+    reweight: bool = False,
+    max_iter: int | None = None,
+    max_iter_rw: int | None = None,
+    eigs: bool = False,
+    debug_briks: bool = False,
+    cumulative_wts: bool = False,
+    verbose: int | None = None,
+    drive_afni: int | None = None,
+    sep_dsets: bool = False,
+    csf_val: float | None = None,
+    min_bad_md: int | None = None,
+    csf_fa: float | None = None,
+    opt: str | None = None,
+    mean_b0: bool = False,
     runner: Runner | None = None,
 ) -> V3dDwitoDtOutputs:
     """
@@ -169,6 +405,43 @@ def v_3d_dwito_dt(
             floats (Gxi, Gyi, Gzi) or a 1D file of b-matrix elements.
         dataset: A 3D bucket dataset with Np+1 sub-briks where the first\
             sub-brik is the volume acquired with no diffusion weighting.
+        prefix: Output dataset prefix name. Default is 'DT'.
+        automask: Mask dataset so that tensors are computed only for\
+            high-intensity (presumably brain) voxels.
+        mask: Use this dataset as mask to include/exclude voxels.
+        bmatrix_nz: Input dataset is b-matrix, not gradient directions, and\
+            there is no row of zeros at the top of the file.
+        bmatrix_z: Similar to '-bmatrix_NZ' but first row of the file is all\
+            zeros.
+        bmatrix_full: Same as '-bmatrix_Z' but with a more intuitive name.
+        scale_out_1000: Increase output parameters with physical units by\
+            multiplying them by 1000.
+        bmax_ref: Flag the reference b-value if it is greater than zero.
+        nonlinear: Compute iterative solution to avoid negative eigenvalues.\
+            This is the default method.
+        linear: Compute simple linear solution.
+        reweight: Recompute weight factors at end of iterations and restart.
+        max_iter: Maximum number of iterations for convergence. Default is 10.
+        max_iter_rw: Max number of iterations after reweighting. Default is 5.
+        eigs: Compute eigenvalues, eigenvectors, fractional anisotropy, and\
+            mean diffusivity in sub-briks 6-19.
+        debug_briks: Add sub-briks with error functional, original error,\
+            number of steps to convergence, and modeled B0 volume.
+        cumulative_wts: Show overall weight factors for each gradient level.
+        verbose: Print convergence steps every nnnnn voxels.
+        drive_afni: Show convergence graphs every nnnnn voxels. AFNI must have\
+            NIML communications on.
+        sep_dsets: Save tensor, eigenvalues, vectors, FA, MD in separate\
+            datasets.
+        csf_val: Assign diffusivity value to DWI data where the mean values for\
+            b=0 volumes is less than the mean of the remaining volumes at each\
+            voxel.
+        min_bad_md: Change the min MD value used as a 'badness check' for\
+            tensor fits.
+        csf_fa: Assign a specific FA value to CSF voxels.
+        opt: Optimization method: 'powell', 'gradient', or 'hybrid'.
+        mean_b0: Use mean of all b=0 volumes for linear computation and initial\
+            linear for nonlinear method.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDwitoDtOutputs`).
@@ -178,6 +451,30 @@ def v_3d_dwito_dt(
     params = v_3d_dwito_dt_params(
         gradient_file=gradient_file,
         dataset=dataset,
+        prefix=prefix,
+        automask=automask,
+        mask=mask,
+        bmatrix_nz=bmatrix_nz,
+        bmatrix_z=bmatrix_z,
+        bmatrix_full=bmatrix_full,
+        scale_out_1000=scale_out_1000,
+        bmax_ref=bmax_ref,
+        nonlinear=nonlinear,
+        linear=linear,
+        reweight=reweight,
+        max_iter=max_iter,
+        max_iter_rw=max_iter_rw,
+        eigs=eigs,
+        debug_briks=debug_briks,
+        cumulative_wts=cumulative_wts,
+        verbose=verbose,
+        drive_afni=drive_afni,
+        sep_dsets=sep_dsets,
+        csf_val=csf_val,
+        min_bad_md=min_bad_md,
+        csf_fa=csf_fa,
+        opt=opt,
+        mean_b0=mean_b0,
     )
     return v_3d_dwito_dt_execute(params, execution)
 

niwrap_afni/afni/v_3d_ecm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ECM_METADATA = Metadata(
-    id="c9bc0ce1e3c30699a348a07653407f3b99801a2a.boutiques",
+    id="fe8e455e00c15b8128839ab77ca8b9a116a3a73b.boutiques",
     name="3dECM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -24,7 +24,9 @@ V3dEcmParameters = typing.TypedDict('V3dEcmParameters', {
     "mask": typing.NotRequired[InputPathType | None],
     "max_iter": typing.NotRequired[int | None],
     "memory": typing.NotRequired[float | None],
+    "num_threads": typing.NotRequired[int | None],
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "out_file": typing.NotRequired[str | None],
     "polort": typing.NotRequired[int | None],
     "scale": typing.NotRequired[float | None],
     "shift": typing.NotRequired[float | None],
@@ -87,7 +89,9 @@ def v_3d_ecm_params(
     mask: InputPathType | None = None,
     max_iter: int | None = None,
     memory: float | None = None,
+    num_threads: int | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    out_file: str | None = None,
     polort: int | None = None,
     scale: float | None = None,
     shift: float | None = None,
@@ -114,7 +118,9 @@ def v_3d_ecm_params(
             iteration; default = 1000.
         memory: Limit memory consumption on system by setting the amount of gb\
             to limit the algorithm to; default = 2gb.
+        num_threads: Set number of threads.
         outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        out_file: Output image file name.
         polort: No description provided.
         scale: Scale correlation coefficients in similarity matrix to after\
             shifting, x >= 0.0; default = 1.0 for -full, 0.5 for -fecm.
@@ -141,8 +147,12 @@ def v_3d_ecm_params(
         params["max_iter"] = max_iter
     if memory is not None:
         params["memory"] = memory
+    if num_threads is not None:
+        params["num_threads"] = num_threads
     if outputtype is not None:
         params["outputtype"] = outputtype
+    if out_file is not None:
+        params["out_file"] = out_file
     if polort is not None:
         params["polort"] = polort
     if scale is not None:
@@ -200,9 +210,15 @@ def v_3d_ecm_cargs(
             "-memory",
             str(params.get("memory"))
         ])
-    cargs.append("[OUT_FILE]")
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
     if params.get("outputtype") is not None:
         cargs.append(params.get("outputtype"))
+    if params.get("out_file") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("out_file")
+        ])
     if params.get("polort") is not None:
         cargs.extend([
             "-polort",
@@ -287,7 +303,9 @@ def v_3d_ecm(
     mask: InputPathType | None = None,
     max_iter: int | None = None,
     memory: float | None = None,
+    num_threads: int | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    out_file: str | None = None,
     polort: int | None = None,
     scale: float | None = None,
     shift: float | None = None,
@@ -320,7 +338,9 @@ def v_3d_ecm(
             iteration; default = 1000.
         memory: Limit memory consumption on system by setting the amount of gb\
             to limit the algorithm to; default = 2gb.
+        num_threads: Set number of threads.
         outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        out_file: Output image file name.
         polort: No description provided.
         scale: Scale correlation coefficients in similarity matrix to after\
             shifting, x >= 0.0; default = 1.0 for -full, 0.5 for -fecm.
@@ -344,7 +364,9 @@ def v_3d_ecm(
         mask=mask,
         max_iter=max_iter,
         memory=memory,
+        num_threads=num_threads,
         outputtype=outputtype,
+        out_file=out_file,
         polort=polort,
         scale=scale,
         shift=shift,

niwrap_afni/afni/v_3d_fdr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_FDR_METADATA = Metadata(
-    id="052b0ab8a12acc2def2e27ee40fa90c4b23263c0.boutiques",
+    id="bfccf66ab83c665d5eb67ddf2fb4fae7d2d9767e.boutiques",
     name="3dFDR",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,7 @@ V_3D_FDR_METADATA = Metadata(
 V3dFdrParameters = typing.TypedDict('V3dFdrParameters', {
     "__STYX_TYPE__": typing.Literal["3dFDR"],
     "input_file": InputPathType,
+    "input1d_file": typing.NotRequired[InputPathType | None],
     "mask_file": typing.NotRequired[InputPathType | None],
     "mask_threshold": typing.NotRequired[float | None],
     "constant_type": typing.NotRequired[typing.Literal["cind", "cdep"] | None],
@@ -80,6 +81,7 @@ class V3dFdrOutputs(typing.NamedTuple):
 def v_3d_fdr_params(
     input_file: InputPathType,
     prefix: str,
+    input1d_file: InputPathType | None = None,
     mask_file: InputPathType | None = None,
     mask_threshold: float | None = None,
     constant_type: typing.Literal["cind", "cdep"] | None = None,
@@ -98,6 +100,7 @@ def v_3d_fdr_params(
     Args:
         input_file: Input 3D functional dataset filename.
         prefix: Use 'pname' for the output dataset prefix name.
+        input1d_file: .1D file containing column of p-values.
         mask_file: Use mask values from file mname. If file mname contains more\
             than 1 sub-brick, the mask sub-brick must be specified. Generally\
             should be used to avoid counting non-brain voxels.
@@ -130,6 +133,8 @@ def v_3d_fdr_params(
         "float": float_,
         "qval": qval,
     }
+    if input1d_file is not None:
+        params["input1d_file"] = input1d_file
     if mask_file is not None:
         params["mask_file"] = mask_file
     if mask_threshold is not None:
@@ -160,6 +165,11 @@ def v_3d_fdr_cargs(
         "-input",
         execution.input_file(params.get("input_file"))
     ])
+    if params.get("input1d_file") is not None:
+        cargs.extend([
+            "-input1D",
+            execution.input_file(params.get("input1d_file"))
+        ])
     if params.get("mask_file") is not None:
         cargs.extend([
             "-mask_file",
@@ -251,6 +261,7 @@ def v_3d_fdr_execute(
 def v_3d_fdr(
     input_file: InputPathType,
     prefix: str,
+    input1d_file: InputPathType | None = None,
     mask_file: InputPathType | None = None,
     mask_threshold: float | None = None,
     constant_type: typing.Literal["cind", "cdep"] | None = None,
@@ -275,6 +286,7 @@ def v_3d_fdr(
     Args:
         input_file: Input 3D functional dataset filename.
         prefix: Use 'pname' for the output dataset prefix name.
+        input1d_file: .1D file containing column of p-values.
         mask_file: Use mask values from file mname. If file mname contains more\
             than 1 sub-brick, the mask sub-brick must be specified. Generally\
             should be used to avoid counting non-brain voxels.
@@ -300,6 +312,7 @@ def v_3d_fdr(
     execution = runner.start_execution(V_3D_FDR_METADATA)
     params = v_3d_fdr_params(
         input_file=input_file,
+        input1d_file=input1d_file,
         mask_file=mask_file,
         mask_threshold=mask_threshold,
         constant_type=constant_type,