niwrap-afni 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_afni/afni/v_3d_warp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WARP_METADATA = Metadata(
-    id="9fc0895546044d51ae3bc018933a57cbeae8baeb.boutiques",
+    id="435289d9d4e3a1653a6f8784ea94d9a8a3aaba92.boutiques",
     name="3dWarp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,27 @@ V_3D_WARP_METADATA = Metadata(
 V3dWarpParameters = typing.TypedDict('V3dWarpParameters', {
     "__STYX_TYPE__": typing.Literal["3dWarp"],
     "dataset": str,
+    "matvec_in2out": typing.NotRequired[InputPathType | None],
+    "matvec_out2in": typing.NotRequired[InputPathType | None],
+    "tta2mni": bool,
+    "mni2tta": bool,
+    "matparent": typing.NotRequired[str | None],
+    "card2oblique": typing.NotRequired[str | None],
+    "oblique_parent": typing.NotRequired[str | None],
+    "deoblique": bool,
+    "oblique2card": bool,
+    "disp_obl_xform_only": bool,
+    "linear": bool,
+    "cubic": bool,
+    "NN": bool,
+    "quintic": bool,
+    "wsinc5": bool,
+    "fsl_matvec": bool,
+    "newgrid": typing.NotRequired[float | None],
+    "gridset": typing.NotRequired[str | None],
+    "zpad": typing.NotRequired[float | None],
+    "verb": bool,
+    "prefix": typing.NotRequired[str | None],
 })
 
 
@@ -60,19 +81,96 @@ class V3dWarpOutputs(typing.NamedTuple):
 
 def v_3d_warp_params(
     dataset: str,
+    matvec_in2out: InputPathType | None = None,
+    matvec_out2in: InputPathType | None = None,
+    tta2mni: bool = False,
+    mni2tta: bool = False,
+    matparent: str | None = None,
+    card2oblique: str | None = None,
+    oblique_parent: str | None = None,
+    deoblique: bool = False,
+    oblique2card: bool = False,
+    disp_obl_xform_only: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    nn: bool = False,
+    quintic: bool = False,
+    wsinc5: bool = False,
+    fsl_matvec: bool = False,
+    newgrid: float | None = None,
+    gridset: str | None = None,
+    zpad: float | None = None,
+    verb: bool = False,
+    prefix: str | None = None,
 ) -> V3dWarpParameters:
     """
     Build parameters.
     
     Args:
         dataset: Input dataset to be warped.
+        matvec_in2out: Read a 3x4 affine transform matrix+vector from file.
+        matvec_out2in: Read a 3x4 affine transform matrix+vector from file.
+        tta2mni: Transform a dataset in Talairach-Tournoux Atlas coordinates to\
+            MNI-152 coordinates.
+        mni2tta: Transform a dataset in MNI-152 coordinates to\
+            Talairach-Tournoux Atlas coordinates.
+        matparent: Read in the matrix from WARPDRIVE_MATVEC_* attributes in the\
+            header of dataset.
+        card2oblique: Make cardinal dataset oblique to match oblique dataset.
+        oblique_parent: Make cardinal dataset oblique to match oblique dataset.
+        deoblique: Transform an oblique dataset to a cardinal dataset.
+        oblique2card: Transform an oblique dataset to a cardinal dataset.
+        disp_obl_xform_only: Display the obliquity transform matrix.
+        linear: Use linear interpolation.
+        cubic: Use cubic interpolation.
+        nn: Use nearest neighbor interpolation.
+        quintic: Use quintic interpolation.
+        wsinc5: Use wsinc5 interpolation.
+        fsl_matvec: Indicates that the matrix file uses FSL ordered coordinates\
+            ('LPI').
+        newgrid: Compute new dataset on a new 3D grid, with specified spacing.
+        gridset: Compute new dataset on the same grid as another dataset.
+        zpad: Pad input dataset with specified planes of zeros on all sides\
+            before transformation.
+        verb: Print out some information along the way.
+        prefix: Set the prefix of the output dataset.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dWarp",
         "dataset": dataset,
+        "tta2mni": tta2mni,
+        "mni2tta": mni2tta,
+        "deoblique": deoblique,
+        "oblique2card": oblique2card,
+        "disp_obl_xform_only": disp_obl_xform_only,
+        "linear": linear,
+        "cubic": cubic,
+        "NN": nn,
+        "quintic": quintic,
+        "wsinc5": wsinc5,
+        "fsl_matvec": fsl_matvec,
+        "verb": verb,
     }
+    if matvec_in2out is not None:
+        params["matvec_in2out"] = matvec_in2out
+    if matvec_out2in is not None:
+        params["matvec_out2in"] = matvec_out2in
+    if matparent is not None:
+        params["matparent"] = matparent
+    if card2oblique is not None:
+        params["card2oblique"] = card2oblique
+    if oblique_parent is not None:
+        params["oblique_parent"] = oblique_parent
+    if newgrid is not None:
+        params["newgrid"] = newgrid
+    if gridset is not None:
+        params["gridset"] = gridset
+    if zpad is not None:
+        params["zpad"] = zpad
+    if prefix is not None:
+        params["prefix"] = prefix
     return params
 
 
@@ -91,8 +189,76 @@ def v_3d_warp_cargs(
     """
     cargs = []
     cargs.append("3dWarp")
-    cargs.append("[OPTIONS]")
     cargs.append(params.get("dataset"))
+    if params.get("matvec_in2out") is not None:
+        cargs.extend([
+            "-matvec_in2out",
+            execution.input_file(params.get("matvec_in2out"))
+        ])
+    if params.get("matvec_out2in") is not None:
+        cargs.extend([
+            "-matvec_out2in",
+            execution.input_file(params.get("matvec_out2in"))
+        ])
+    if params.get("tta2mni"):
+        cargs.append("-tta2mni")
+    if params.get("mni2tta"):
+        cargs.append("-mni2tta")
+    if params.get("matparent") is not None:
+        cargs.extend([
+            "-matparent",
+            params.get("matparent")
+        ])
+    if params.get("card2oblique") is not None:
+        cargs.extend([
+            "-card2oblique",
+            params.get("card2oblique")
+        ])
+    if params.get("oblique_parent") is not None:
+        cargs.extend([
+            "-oblique_parent",
+            params.get("oblique_parent")
+        ])
+    if params.get("deoblique"):
+        cargs.append("-deoblique")
+    if params.get("oblique2card"):
+        cargs.append("-oblique2card")
+    if params.get("disp_obl_xform_only"):
+        cargs.append("-disp_obl_xform_only")
+    if params.get("linear"):
+        cargs.append("-linear")
+    if params.get("cubic"):
+        cargs.append("-cubic")
+    if params.get("NN"):
+        cargs.append("-NN")
+    if params.get("quintic"):
+        cargs.append("-quintic")
+    if params.get("wsinc5"):
+        cargs.append("-wsinc5")
+    if params.get("fsl_matvec"):
+        cargs.append("-fsl_matvec")
+    if params.get("newgrid") is not None:
+        cargs.extend([
+            "-newgrid",
+            str(params.get("newgrid"))
+        ])
+    if params.get("gridset") is not None:
+        cargs.extend([
+            "-gridset",
+            params.get("gridset")
+        ])
+    if params.get("zpad") is not None:
+        cargs.extend([
+            "-zpad",
+            str(params.get("zpad"))
+        ])
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
     return cargs
 
 
@@ -141,6 +307,27 @@ def v_3d_warp_execute(
 
 def v_3d_warp(
     dataset: str,
+    matvec_in2out: InputPathType | None = None,
+    matvec_out2in: InputPathType | None = None,
+    tta2mni: bool = False,
+    mni2tta: bool = False,
+    matparent: str | None = None,
+    card2oblique: str | None = None,
+    oblique_parent: str | None = None,
+    deoblique: bool = False,
+    oblique2card: bool = False,
+    disp_obl_xform_only: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    nn: bool = False,
+    quintic: bool = False,
+    wsinc5: bool = False,
+    fsl_matvec: bool = False,
+    newgrid: float | None = None,
+    gridset: str | None = None,
+    zpad: float | None = None,
+    verb: bool = False,
+    prefix: str | None = None,
     runner: Runner | None = None,
 ) -> V3dWarpOutputs:
     """
@@ -152,6 +339,32 @@ def v_3d_warp(
     
     Args:
         dataset: Input dataset to be warped.
+        matvec_in2out: Read a 3x4 affine transform matrix+vector from file.
+        matvec_out2in: Read a 3x4 affine transform matrix+vector from file.
+        tta2mni: Transform a dataset in Talairach-Tournoux Atlas coordinates to\
+            MNI-152 coordinates.
+        mni2tta: Transform a dataset in MNI-152 coordinates to\
+            Talairach-Tournoux Atlas coordinates.
+        matparent: Read in the matrix from WARPDRIVE_MATVEC_* attributes in the\
+            header of dataset.
+        card2oblique: Make cardinal dataset oblique to match oblique dataset.
+        oblique_parent: Make cardinal dataset oblique to match oblique dataset.
+        deoblique: Transform an oblique dataset to a cardinal dataset.
+        oblique2card: Transform an oblique dataset to a cardinal dataset.
+        disp_obl_xform_only: Display the obliquity transform matrix.
+        linear: Use linear interpolation.
+        cubic: Use cubic interpolation.
+        nn: Use nearest neighbor interpolation.
+        quintic: Use quintic interpolation.
+        wsinc5: Use wsinc5 interpolation.
+        fsl_matvec: Indicates that the matrix file uses FSL ordered coordinates\
+            ('LPI').
+        newgrid: Compute new dataset on a new 3D grid, with specified spacing.
+        gridset: Compute new dataset on the same grid as another dataset.
+        zpad: Pad input dataset with specified planes of zeros on all sides\
+            before transformation.
+        verb: Print out some information along the way.
+        prefix: Set the prefix of the output dataset.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dWarpOutputs`).
@@ -160,6 +373,27 @@ def v_3d_warp(
     execution = runner.start_execution(V_3D_WARP_METADATA)
     params = v_3d_warp_params(
         dataset=dataset,
+        matvec_in2out=matvec_in2out,
+        matvec_out2in=matvec_out2in,
+        tta2mni=tta2mni,
+        mni2tta=mni2tta,
+        matparent=matparent,
+        card2oblique=card2oblique,
+        oblique_parent=oblique_parent,
+        deoblique=deoblique,
+        oblique2card=oblique2card,
+        disp_obl_xform_only=disp_obl_xform_only,
+        linear=linear,
+        cubic=cubic,
+        nn=nn,
+        quintic=quintic,
+        wsinc5=wsinc5,
+        fsl_matvec=fsl_matvec,
+        newgrid=newgrid,
+        gridset=gridset,
+        zpad=zpad,
+        verb=verb,
+        prefix=prefix,
     )
     return v_3d_warp_execute(params, execution)
 

niwrap_afni/afni/v_3d_wilcoxon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WILCOXON_METADATA = Metadata(
-    id="463bd0c7f172cd1b8be0a6f1adaeefb51a0010ea.boutiques",
+    id="ab0873d1df66a8478516e2a9302c8e42a90d10ec.boutiques",
     name="3dWilcoxon",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -125,12 +125,14 @@ def v_3d_wilcoxon_cargs(
             "-voxel",
             str(params.get("voxel"))
         ])
-    cargs.append("-dset")
-    cargs.append("1")
-    cargs.extend([execution.input_file(f) for f in params.get("dset1_x")])
-    cargs.append("-dset")
-    cargs.append("2")
-    cargs.extend([execution.input_file(f) for f in params.get("dset2_y")])
+    cargs.extend([
+        "-dset 1",
+        *[execution.input_file(f) for f in params.get("dset1_x")]
+    ])
+    cargs.extend([
+        "-dset 2",
+        *[execution.input_file(f) for f in params.get("dset2_y")]
+    ])
     cargs.extend([
         "-out",
         params.get("output_prefix")

niwrap_afni/afni/v_3dbucket.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DBUCKET_METADATA = Metadata(
-    id="a07bb3d6d6114eb899f05be41e593f262e6cd274.boutiques",
+    id="24263e7460b92cc3d7edf73c1101058593a99f03.boutiques",
     name="3dbucket",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,7 @@ V_3DBUCKET_METADATA = Metadata(
 V3dbucketParameters = typing.TypedDict('V3dbucketParameters', {
     "__STYX_TYPE__": typing.Literal["3dbucket"],
     "prefix": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
     "session": typing.NotRequired[str | None],
     "glueto": typing.NotRequired[str | None],
     "aglueto": typing.NotRequired[str | None],
@@ -69,6 +70,7 @@ class V3dbucketOutputs(typing.NamedTuple):
 def v_3dbucket_params(
     input_files: list[str],
     prefix: str | None = None,
+    output: str | None = None,
     session: str | None = None,
     glueto: str | None = None,
     aglueto: str | None = None,
@@ -83,6 +85,7 @@ def v_3dbucket_params(
     Args:
         input_files: Input datasets with optional sub-brick selection.
         prefix: Use 'pname' for the output dataset prefix name.
+        output: Use 'pname' for the output dataset prefix name.
         session: Use 'dir' for the output dataset session directory.\
             [default='./'=current working directory].
         glueto: Append bricks to the end of the 'fname' dataset.
@@ -106,6 +109,8 @@ def v_3dbucket_params(
     }
     if prefix is not None:
         params["prefix"] = prefix
+    if output is not None:
+        params["output"] = output
     if session is not None:
         params["session"] = session
     if glueto is not None:
@@ -135,6 +140,11 @@ def v_3dbucket_cargs(
             "-prefix",
             params.get("prefix")
         ])
+    if params.get("output") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output")
+        ])
     if params.get("session") is not None:
         cargs.extend([
             "-session",
@@ -208,6 +218,7 @@ def v_3dbucket_execute(
 def v_3dbucket(
     input_files: list[str],
     prefix: str | None = None,
+    output: str | None = None,
     session: str | None = None,
     glueto: str | None = None,
     aglueto: str | None = None,
@@ -227,6 +238,7 @@ def v_3dbucket(
     Args:
         input_files: Input datasets with optional sub-brick selection.
         prefix: Use 'pname' for the output dataset prefix name.
+        output: Use 'pname' for the output dataset prefix name.
         session: Use 'dir' for the output dataset session directory.\
             [default='./'=current working directory].
         glueto: Append bricks to the end of the 'fname' dataset.
@@ -245,6 +257,7 @@ def v_3dbucket(
     execution = runner.start_execution(V_3DBUCKET_METADATA)
     params = v_3dbucket_params(
         prefix=prefix,
+        output=output,
         session=session,
         glueto=glueto,
         aglueto=aglueto,

niwrap_afni/afni/v_3dcalc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DCALC_METADATA = Metadata(
-    id="3a17cb5cc1d3b991065054ac23d926bf8d3018c8.boutiques",
+    id="8562822f45d27f4c091ec9137e9dfa4943f96f87.boutiques",
     name="3dcalc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",

niwrap_afni/afni/v_3dcopy.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DCOPY_METADATA = Metadata(
-    id="4b8187d004c6f4ba95518e709ad1f9b3eb4ed322.boutiques",
+    id="cf613edf42ba1934d2ac712d37faeb09217cdd61.boutiques",
     name="3dcopy",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,9 @@ V3dcopyParameters = typing.TypedDict('V3dcopyParameters', {
     "__STYX_TYPE__": typing.Literal["3dcopy"],
     "verbose": bool,
     "denote": bool,
+    "old_prefix": str,
+    "view": typing.NotRequired[str | None],
+    "new_prefix": str,
 })
 
 
@@ -60,15 +63,22 @@ class V3dcopyOutputs(typing.NamedTuple):
 
 
 def v_3dcopy_params(
+    old_prefix: str,
+    new_prefix: str,
     verbose: bool = False,
     denote: bool = False,
+    view: str | None = None,
 ) -> V3dcopyParameters:
     """
     Build parameters.
     
     Args:
+        old_prefix: Old dataset prefix (and view if specific dataset view is to\
+            be copied).
+        new_prefix: New dataset prefix or directory path.
         verbose: Print progress reports.
         denote: Remove any Notes from the file.
+        view: Specified view (orig, acpc, tlrc).
     Returns:
         Parameter dictionary
     """
@@ -76,7 +86,11 @@ def v_3dcopy_params(
         "__STYXTYPE__": "3dcopy",
         "verbose": verbose,
         "denote": denote,
+        "old_prefix": old_prefix,
+        "new_prefix": new_prefix,
     }
+    if view is not None:
+        params["view"] = view
     return params
 
 
@@ -99,8 +113,12 @@ def v_3dcopy_cargs(
         cargs.append("-verb")
     if params.get("denote"):
         cargs.append("-denote")
-    cargs.append("{OLD_PREFIX}+{VIEW}")
-    cargs.append("{NEW_PREFIX}")
+    if params.get("view") is not None:
+        cargs.extend([
+            "+",
+            params.get("old_prefix") + params.get("view")
+        ])
+    cargs.append(params.get("new_prefix"))
     return cargs
 
 
@@ -148,8 +166,11 @@ def v_3dcopy_execute(
 
 
 def v_3dcopy(
+    old_prefix: str,
+    new_prefix: str,
     verbose: bool = False,
     denote: bool = False,
+    view: str | None = None,
     runner: Runner | None = None,
 ) -> V3dcopyOutputs:
     """
@@ -160,8 +181,12 @@ def v_3dcopy(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        old_prefix: Old dataset prefix (and view if specific dataset view is to\
+            be copied).
+        new_prefix: New dataset prefix or directory path.
         verbose: Print progress reports.
         denote: Remove any Notes from the file.
+        view: Specified view (orig, acpc, tlrc).
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dcopyOutputs`).
@@ -171,6 +196,9 @@ def v_3dcopy(
     params = v_3dcopy_params(
         verbose=verbose,
         denote=denote,
+        old_prefix=old_prefix,
+        view=view,
+        new_prefix=new_prefix,
     )
     return v_3dcopy_execute(params, execution)
 

niwrap_afni/afni/v_3dmask_svd.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMASK_SVD_METADATA = Metadata(
-    id="5cc0ef9b4df81bcbe1689588ddbddf9e81594730.boutiques",
+    id="eecbee0a49ddb248abb1a5cc5b60e995c855df15.boutiques",
     name="3dmaskSVD",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,14 @@ V_3DMASK_SVD_METADATA = Metadata(
 V3dmaskSvdParameters = typing.TypedDict('V3dmaskSvdParameters', {
     "__STYX_TYPE__": typing.Literal["3dmaskSVD"],
     "input_dataset": InputPathType,
+    "vnorm": bool,
+    "sval": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "polort": typing.NotRequired[float | None],
+    "bandpass": typing.NotRequired[list[str] | None],
+    "ort": typing.NotRequired[list[InputPathType] | None],
+    "alt_input": typing.NotRequired[InputPathType | None],
 })
 
 
@@ -63,19 +71,50 @@ class V3dmaskSvdOutputs(typing.NamedTuple):
 
 def v_3dmask_svd_params(
     input_dataset: InputPathType,
+    vnorm: bool = False,
+    sval: float | None = None,
+    mask_file: InputPathType | None = None,
+    automask: bool = False,
+    polort: float | None = None,
+    bandpass: list[str] | None = None,
+    ort: list[InputPathType] | None = None,
+    alt_input: InputPathType | None = None,
 ) -> V3dmaskSvdParameters:
     """
     Build parameters.
     
     Args:
         input_dataset: Input dataset.
+        vnorm: L2 normalize all time series before SVD.
+        sval: Output singular vectors 0 .. a (default a=0 = first one only).
+        mask_file: Define the mask (default is entire dataset).
+        automask: Automatic mask definition.
+        polort: Remove polynomial trend (default 0 if not specified).
+        bandpass: Bandpass filter (mutually exclusive with -polort).
+        ort: Time series to remove from the data before SVD-ization. You can\
+            give more than 1 '-ort' option. 'xx.1D' can contain more than 1 column.
+        alt_input: Alternative way to give the input dataset name.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dmaskSVD",
         "input_dataset": input_dataset,
+        "vnorm": vnorm,
+        "automask": automask,
     }
+    if sval is not None:
+        params["sval"] = sval
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if polort is not None:
+        params["polort"] = polort
+    if bandpass is not None:
+        params["bandpass"] = bandpass
+    if ort is not None:
+        params["ort"] = ort
+    if alt_input is not None:
+        params["alt_input"] = alt_input
     return params
 
 
@@ -94,8 +133,41 @@ def v_3dmask_svd_cargs(
     """
     cargs = []
     cargs.append("3dmaskSVD")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("vnorm"):
+        cargs.append("-vnorm")
+    if params.get("sval") is not None:
+        cargs.extend([
+            "-sval",
+            str(params.get("sval"))
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("bandpass") is not None:
+        cargs.extend([
+            "-bpass",
+            *params.get("bandpass")
+        ])
+    if params.get("ort") is not None:
+        cargs.extend([
+            "-ort",
+            *[execution.input_file(f) for f in params.get("ort")]
+        ])
+    if params.get("alt_input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("alt_input"))
+        ])
     return cargs
 
 
@@ -146,6 +218,14 @@ def v_3dmask_svd_execute(
 
 def v_3dmask_svd(
     input_dataset: InputPathType,
+    vnorm: bool = False,
+    sval: float | None = None,
+    mask_file: InputPathType | None = None,
+    automask: bool = False,
+    polort: float | None = None,
+    bandpass: list[str] | None = None,
+    ort: list[InputPathType] | None = None,
+    alt_input: InputPathType | None = None,
     runner: Runner | None = None,
 ) -> V3dmaskSvdOutputs:
     """
@@ -158,6 +238,15 @@ def v_3dmask_svd(
     
     Args:
         input_dataset: Input dataset.
+        vnorm: L2 normalize all time series before SVD.
+        sval: Output singular vectors 0 .. a (default a=0 = first one only).
+        mask_file: Define the mask (default is entire dataset).
+        automask: Automatic mask definition.
+        polort: Remove polynomial trend (default 0 if not specified).
+        bandpass: Bandpass filter (mutually exclusive with -polort).
+        ort: Time series to remove from the data before SVD-ization. You can\
+            give more than 1 '-ort' option. 'xx.1D' can contain more than 1 column.
+        alt_input: Alternative way to give the input dataset name.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmaskSvdOutputs`).
@@ -166,6 +255,14 @@ def v_3dmask_svd(
     execution = runner.start_execution(V_3DMASK_SVD_METADATA)
     params = v_3dmask_svd_params(
         input_dataset=input_dataset,
+        vnorm=vnorm,
+        sval=sval,
+        mask_file=mask_file,
+        automask=automask,
+        polort=polort,
+        bandpass=bandpass,
+        ort=ort,
+        alt_input=alt_input,
     )
     return v_3dmask_svd_execute(params, execution)