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

niwrap_afni/afni/v_1d_sem.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_SEM_METADATA = Metadata(
-    id="22951ac5931e28304cde031a44c651e57c4e4a1e.boutiques",
+    id="a26930914a15136a68f2004d57838df7d226dcb0.boutiques",
     name="1dSEM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,6 +19,18 @@ V1dSemParameters = typing.TypedDict('V1dSemParameters', {
     "correlation_matrix": InputPathType,
     "residual_variance": InputPathType,
     "degrees_of_freedom": float,
+    "max_iterations": typing.NotRequired[int | None],
+    "number_random_trials": typing.NotRequired[int | None],
+    "limits": typing.NotRequired[list[float] | None],
+    "calculate_cost": bool,
+    "verbose": typing.NotRequired[int | None],
+    "tree_growth": bool,
+    "model_search": bool,
+    "max_paths": typing.NotRequired[int | None],
+    "stop_cost": typing.NotRequired[float | None],
+    "forest_growth": bool,
+    "grow_all": bool,
+    "leafpicker": bool,
 })
 
 
@@ -69,6 +81,18 @@ def v_1d_sem_params(
     correlation_matrix: InputPathType,
     residual_variance: InputPathType,
     degrees_of_freedom: float,
+    max_iterations: int | None = None,
+    number_random_trials: int | None = None,
+    limits: list[float] | None = None,
+    calculate_cost: bool = False,
+    verbose: int | None = None,
+    tree_growth: bool = False,
+    model_search: bool = False,
+    max_paths: int | None = None,
+    stop_cost: float | None = None,
+    forest_growth: bool = False,
+    grow_all: bool = False,
+    leafpicker: bool = False,
 ) -> V1dSemParameters:
     """
     Build parameters.
@@ -78,6 +102,30 @@ def v_1d_sem_params(
         correlation_matrix: Correlation matrix 1D file.
         residual_variance: Residual variance vector 1D file.
         degrees_of_freedom: Degrees of freedom.
+        max_iterations: Maximum number of iterations for convergence\
+            (Default=10000). Values can range from 1 to any positive integer less\
+            than 10000.
+        number_random_trials: Number of random trials before optimization\
+            (Default = 100).
+        limits: Lower and upper limits for connection coefficients (Default =\
+            -1.0 to 1.0).
+        calculate_cost: No modeling at all, just calculate the cost function\
+            for the coefficients as given in the theta file.
+        verbose: Print info every nnnnn steps.
+        tree_growth: Search for best model by growing a model for one\
+            additional coefficient from the previous model for n-1 coefficients.
+        model_search: Search for best model by growing a model for one\
+            additional coefficient from the previous model for n-1 coefficients.
+        max_paths: Maximum number of paths to include (Default = 1000).
+        stop_cost: Stop searching for paths when cost function is below this\
+            value (Default = 0.1).
+        forest_growth: Search over all possible models by comparing models at\
+            incrementally increasing number of path coefficients.
+        grow_all: Search over all possible models by comparing models at\
+            incrementally increasing number of path coefficients.
+        leafpicker: Expands the search optimization to look at multiple paths\
+            to avoid local minimum. This method is the default technique for tree\
+            growth and standard coefficient searches.
     Returns:
         Parameter dictionary
     """
@@ -87,7 +135,25 @@ def v_1d_sem_params(
         "correlation_matrix": correlation_matrix,
         "residual_variance": residual_variance,
         "degrees_of_freedom": degrees_of_freedom,
+        "calculate_cost": calculate_cost,
+        "tree_growth": tree_growth,
+        "model_search": model_search,
+        "forest_growth": forest_growth,
+        "grow_all": grow_all,
+        "leafpicker": leafpicker,
     }
+    if max_iterations is not None:
+        params["max_iterations"] = max_iterations
+    if number_random_trials is not None:
+        params["number_random_trials"] = number_random_trials
+    if limits is not None:
+        params["limits"] = limits
+    if verbose is not None:
+        params["verbose"] = verbose
+    if max_paths is not None:
+        params["max_paths"] = max_paths
+    if stop_cost is not None:
+        params["stop_cost"] = stop_cost
     return params
 
 
@@ -122,7 +188,48 @@ def v_1d_sem_cargs(
         "-DF",
         str(params.get("degrees_of_freedom"))
     ])
-    cargs.append("[OPTIONS]")
+    if params.get("max_iterations") is not None:
+        cargs.extend([
+            "-max_iter",
+            str(params.get("max_iterations"))
+        ])
+    if params.get("number_random_trials") is not None:
+        cargs.extend([
+            "-nrand",
+            str(params.get("number_random_trials"))
+        ])
+    if params.get("limits") is not None:
+        cargs.extend([
+            "-limits",
+            *map(str, params.get("limits"))
+        ])
+    if params.get("calculate_cost"):
+        cargs.append("-calccost")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verbose",
+            str(params.get("verbose"))
+        ])
+    if params.get("tree_growth"):
+        cargs.append("-tree_growth")
+    if params.get("model_search"):
+        cargs.append("-model_search")
+    if params.get("max_paths") is not None:
+        cargs.extend([
+            "-max_paths",
+            str(params.get("max_paths"))
+        ])
+    if params.get("stop_cost") is not None:
+        cargs.extend([
+            "-stop_cost",
+            str(params.get("stop_cost"))
+        ])
+    if params.get("forest_growth"):
+        cargs.append("-forest_growth")
+    if params.get("grow_all"):
+        cargs.append("-grow_all")
+    if params.get("leafpicker"):
+        cargs.append("-leafpicker")
     return cargs
 
 
@@ -176,6 +283,18 @@ def v_1d_sem(
     correlation_matrix: InputPathType,
     residual_variance: InputPathType,
     degrees_of_freedom: float,
+    max_iterations: int | None = None,
+    number_random_trials: int | None = None,
+    limits: list[float] | None = None,
+    calculate_cost: bool = False,
+    verbose: int | None = None,
+    tree_growth: bool = False,
+    model_search: bool = False,
+    max_paths: int | None = None,
+    stop_cost: float | None = None,
+    forest_growth: bool = False,
+    grow_all: bool = False,
+    leafpicker: bool = False,
     runner: Runner | None = None,
 ) -> V1dSemOutputs:
     """
@@ -191,6 +310,30 @@ def v_1d_sem(
         correlation_matrix: Correlation matrix 1D file.
         residual_variance: Residual variance vector 1D file.
         degrees_of_freedom: Degrees of freedom.
+        max_iterations: Maximum number of iterations for convergence\
+            (Default=10000). Values can range from 1 to any positive integer less\
+            than 10000.
+        number_random_trials: Number of random trials before optimization\
+            (Default = 100).
+        limits: Lower and upper limits for connection coefficients (Default =\
+            -1.0 to 1.0).
+        calculate_cost: No modeling at all, just calculate the cost function\
+            for the coefficients as given in the theta file.
+        verbose: Print info every nnnnn steps.
+        tree_growth: Search for best model by growing a model for one\
+            additional coefficient from the previous model for n-1 coefficients.
+        model_search: Search for best model by growing a model for one\
+            additional coefficient from the previous model for n-1 coefficients.
+        max_paths: Maximum number of paths to include (Default = 1000).
+        stop_cost: Stop searching for paths when cost function is below this\
+            value (Default = 0.1).
+        forest_growth: Search over all possible models by comparing models at\
+            incrementally increasing number of path coefficients.
+        grow_all: Search over all possible models by comparing models at\
+            incrementally increasing number of path coefficients.
+        leafpicker: Expands the search optimization to look at multiple paths\
+            to avoid local minimum. This method is the default technique for tree\
+            growth and standard coefficient searches.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dSemOutputs`).
@@ -202,6 +345,18 @@ def v_1d_sem(
         correlation_matrix=correlation_matrix,
         residual_variance=residual_variance,
         degrees_of_freedom=degrees_of_freedom,
+        max_iterations=max_iterations,
+        number_random_trials=number_random_trials,
+        limits=limits,
+        calculate_cost=calculate_cost,
+        verbose=verbose,
+        tree_growth=tree_growth,
+        model_search=model_search,
+        max_paths=max_paths,
+        stop_cost=stop_cost,
+        forest_growth=forest_growth,
+        grow_all=grow_all,
+        leafpicker=leafpicker,
     )
     return v_1d_sem_execute(params, execution)
 

niwrap_afni/afni/v_1d_tsort.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_TSORT_METADATA = Metadata(
-    id="731309e5236007bd69df120b6a0494a5de798eeb.boutiques",
+    id="f4d144dd2a33cb2a0c2516cb757ba2a8c82c7262.boutiques",
     name="1dTsort",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,7 @@ V_1D_TSORT_METADATA = Metadata(
 
 V1dTsortParameters = typing.TypedDict('V1dTsortParameters', {
     "__STYX_TYPE__": typing.Literal["1dTsort"],
+    "inc_order": bool,
     "dec_order": bool,
     "transpose": bool,
     "column": typing.NotRequired[float | None],
@@ -64,6 +65,7 @@ class V1dTsortOutputs(typing.NamedTuple):
 
 def v_1d_tsort_params(
     infile: InputPathType,
+    inc_order: bool = False,
     dec_order: bool = False,
     transpose: bool = False,
     column: float | None = None,
@@ -74,6 +76,7 @@ def v_1d_tsort_params(
     
     Args:
         infile: Input 1D file to be sorted.
+        inc_order: Sort into increasing order [default].
         dec_order: Sort into decreasing order.
         transpose: Transpose the file before output.
         column: Sort only on column #j (counting starts at 0), and carry the\
@@ -85,6 +88,7 @@ def v_1d_tsort_params(
     """
     params = {
         "__STYXTYPE__": "1dTsort",
+        "inc_order": inc_order,
         "dec_order": dec_order,
         "transpose": transpose,
         "imode": imode,
@@ -110,6 +114,8 @@ def v_1d_tsort_cargs(
     """
     cargs = []
     cargs.append("1dTsort")
+    if params.get("inc_order"):
+        cargs.append("-inc")
     if params.get("dec_order"):
         cargs.append("-dec")
     if params.get("transpose"):
@@ -170,6 +176,7 @@ def v_1d_tsort_execute(
 
 def v_1d_tsort(
     infile: InputPathType,
+    inc_order: bool = False,
     dec_order: bool = False,
     transpose: bool = False,
     column: float | None = None,
@@ -185,6 +192,7 @@ def v_1d_tsort(
     
     Args:
         infile: Input 1D file to be sorted.
+        inc_order: Sort into increasing order [default].
         dec_order: Sort into decreasing order.
         transpose: Transpose the file before output.
         column: Sort only on column #j (counting starts at 0), and carry the\
@@ -198,6 +206,7 @@ def v_1d_tsort(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_1D_TSORT_METADATA)
     params = v_1d_tsort_params(
+        inc_order=inc_order,
         dec_order=dec_order,
         transpose=transpose,
         column=column,

niwrap_afni/afni/v_1ddot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1DDOT_METADATA = Metadata(
-    id="89e3bea294b27fb22b4f6d2f28db83dbf8daea66.boutiques",
+    id="3b57cf09716c42dc28cccea1c8b49a4f626abd0b.boutiques",
     name="1ddot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -64,6 +64,8 @@ class V1ddotOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
+    stdout: list[str]
+    """output text file"""
     stdout_output: OutputPathType
     """Output correlation or covariance matrix printed to stdout."""
 
@@ -140,8 +142,6 @@ def v_1ddot_cargs(
     if params.get("okzero_flag"):
         cargs.append("-okzero")
     cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    cargs.append(">")
-    cargs.append("stdout.txt")
     return cargs
 
 
@@ -160,6 +160,7 @@ def v_1ddot_outputs(
     """
     ret = V1ddotOutputs(
         root=execution.output_file("."),
+        stdout=[],
         stdout_output=execution.output_file("stdout.txt"),
     )
     return ret
@@ -186,7 +187,7 @@ def v_1ddot_execute(
     params = execution.params(params)
     cargs = v_1ddot_cargs(params, execution)
     ret = v_1ddot_outputs(params, execution)
-    execution.run(cargs)
+    execution.run(cargs, handle_stdout=lambda s: ret.stdout.append(s))
     return ret
 
 

niwrap_afni/afni/v_1deval.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1DEVAL_METADATA = Metadata(
-    id="da64e5acb6bc6cd359ef137e00f938392ac2b5e3.boutiques",
+    id="4d289385c575fb0e342e48148cb17a3c5cbf7c68.boutiques",
     name="1deval",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -21,6 +21,7 @@ V1devalParameters = typing.TypedDict('V1devalParameters', {
     "index": typing.NotRequired[InputPathType | None],
     "1D": bool,
     "symbols": typing.NotRequired[list[InputPathType] | None],
+    "symbol_values": typing.NotRequired[list[str] | None],
     "expression": str,
 })
 
@@ -75,6 +76,7 @@ def v_1deval_params(
     index: InputPathType | None = None,
     v_1_d: bool = False,
     symbols: list[InputPathType] | None = None,
+    symbol_values: list[str] | None = None,
 ) -> V1devalParameters:
     """
     Build parameters.
@@ -92,6 +94,8 @@ def v_1deval_params(
             input on the command line of another program.
         symbols: Read time series file and assign it to the symbol 'a'. Letters\
             'a' to 'z' may be used as symbols.
+        symbol_values: Assign a fixed numerical value to the symbol 'a'.\
+            Letters 'a' to 'z' may be used as symbols.
     Returns:
         Parameter dictionary
     """
@@ -110,6 +114,8 @@ def v_1deval_params(
         params["index"] = index
     if symbols is not None:
         params["symbols"] = symbols
+    if symbol_values is not None:
+        params["symbol_values"] = symbol_values
     return params
 
 
@@ -155,6 +161,11 @@ def v_1deval_cargs(
             "-a",
             *[execution.input_file(f) for f in params.get("symbols")]
         ])
+    if params.get("symbol_values") is not None:
+        cargs.extend([
+            "-a=",
+            *params.get("symbol_values")
+        ])
     cargs.extend([
         "-expr",
         params.get("expression")
@@ -215,6 +226,7 @@ def v_1deval(
     index: InputPathType | None = None,
     v_1_d: bool = False,
     symbols: list[InputPathType] | None = None,
+    symbol_values: list[str] | None = None,
     runner: Runner | None = None,
 ) -> V1devalOutputs:
     """
@@ -238,6 +250,8 @@ def v_1deval(
             input on the command line of another program.
         symbols: Read time series file and assign it to the symbol 'a'. Letters\
             'a' to 'z' may be used as symbols.
+        symbol_values: Assign a fixed numerical value to the symbol 'a'.\
+            Letters 'a' to 'z' may be used as symbols.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1devalOutputs`).
@@ -251,6 +265,7 @@ def v_1deval(
         index=index,
         v_1_d=v_1_d,
         symbols=symbols,
+        symbol_values=symbol_values,
         expression=expression,
     )
     return v_1deval_execute(params, execution)

niwrap_afni/afni/v_1dgen_arma11.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1DGEN_ARMA11_METADATA = Metadata(
-    id="9fce1559df8cc31e0d2c99d44319f7a47b38ba76.boutiques",
+    id="db531d2478af899030ee6f05096f794916316ef9.boutiques",
     name="1dgenARMA11",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,7 @@ V_1DGEN_ARMA11_METADATA = Metadata(
 
 V1dgenArma11Parameters = typing.TypedDict('V1dgenArma11Parameters', {
     "__STYX_TYPE__": typing.Literal["1dgenARMA11"],
+    "length": typing.NotRequired[float | None],
     "length_alt": typing.NotRequired[float | None],
     "num_series": typing.NotRequired[float | None],
     "param_a": typing.NotRequired[float | None],
@@ -72,6 +73,7 @@ class V1dgenArma11Outputs(typing.NamedTuple):
 
 
 def v_1dgen_arma11_params(
+    length: float | None = None,
     length_alt: float | None = None,
     num_series: float | None = None,
     param_a: float | None = None,
@@ -88,6 +90,8 @@ def v_1dgen_arma11_params(
     Build parameters.
     
     Args:
+        length: Specify the length of the time series vector to generate\
+            (equivalent to -len option).
         length_alt: Specify the length of the time series vector to generate\
             (equivalent to -num option).
         num_series: The number of time series vectors to generate; defaults to\
@@ -111,6 +115,8 @@ def v_1dgen_arma11_params(
         "__STYXTYPE__": "1dgenARMA11",
         "normalize": normalize,
     }
+    if length is not None:
+        params["length"] = length
     if length_alt is not None:
         params["length_alt"] = length_alt
     if num_series is not None:
@@ -149,6 +155,11 @@ def v_1dgen_arma11_cargs(
     """
     cargs = []
     cargs.append("1dgenARMA11")
+    if params.get("length") is not None:
+        cargs.extend([
+            "-num",
+            str(params.get("length"))
+        ])
     if params.get("length_alt") is not None:
         cargs.extend([
             "-len",
@@ -250,6 +261,7 @@ def v_1dgen_arma11_execute(
 
 
 def v_1dgen_arma11(
+    length: float | None = None,
     length_alt: float | None = None,
     num_series: float | None = None,
     param_a: float | None = None,
@@ -272,6 +284,8 @@ def v_1dgen_arma11(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        length: Specify the length of the time series vector to generate\
+            (equivalent to -len option).
         length_alt: Specify the length of the time series vector to generate\
             (equivalent to -num option).
         num_series: The number of time series vectors to generate; defaults to\
@@ -295,6 +309,7 @@ def v_1dgen_arma11(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_1DGEN_ARMA11_METADATA)
     params = v_1dgen_arma11_params(
+        length=length,
         length_alt=length_alt,
         num_series=num_series,
         param_a=param_a,

niwrap_afni/afni/v_3_droimaker.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3_DROIMAKER_METADATA = Metadata(
-    id="52994e672a5f137f27dbb8bbd59f66cee7093ffe.boutiques",
+    id="16b5bd8ed0bd228cb0f4654876f7baea2f4af429.boutiques",
     name="3DROIMaker",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -20,6 +20,7 @@ V3DroimakerParameters = typing.TypedDict('V3DroimakerParameters', {
     "prefix": str,
     "refset": typing.NotRequired[InputPathType | None],
     "volthr": typing.NotRequired[float | None],
+    "only_some_top": typing.NotRequired[float | None],
     "only_conn_top": typing.NotRequired[float | None],
     "inflate": typing.NotRequired[float | None],
     "trim_off_wm": bool,
@@ -89,6 +90,7 @@ def v_3_droimaker_params(
     prefix: str,
     refset: InputPathType | None = None,
     volthr: float | None = None,
+    only_some_top: float | None = None,
     only_conn_top: float | None = None,
     inflate: float | None = None,
     trim_off_wm: bool = False,
@@ -118,6 +120,8 @@ def v_3_droimaker_params(
             which to label specific GM ROIs after thresholding.
         volthr: Minimum size a cluster of voxels must have in order to remain a\
             GM ROI after thresholding. Can reduce 'noisy' clusters.
+        only_some_top: Restrict each found region to keep only N voxels with\
+            the highest inset values.
         only_conn_top: Select N max contiguous voxels in a region starting from\
             peak voxel and expanding.
         inflate: Number of voxels to pad each found ROI in order to turn GM\
@@ -161,6 +165,8 @@ def v_3_droimaker_params(
         params["refset"] = refset
     if volthr is not None:
         params["volthr"] = volthr
+    if only_some_top is not None:
+        params["only_some_top"] = only_some_top
     if only_conn_top is not None:
         params["only_conn_top"] = only_conn_top
     if inflate is not None:
@@ -214,6 +220,11 @@ def v_3_droimaker_cargs(
             "-volthr",
             str(params.get("volthr"))
         ])
+    if params.get("only_some_top") is not None:
+        cargs.extend([
+            "-only_some_top",
+            str(params.get("only_some_top"))
+        ])
     if params.get("only_conn_top") is not None:
         cargs.extend([
             "-only_conn_top",
@@ -321,6 +332,7 @@ def v_3_droimaker(
     prefix: str,
     refset: InputPathType | None = None,
     volthr: float | None = None,
+    only_some_top: float | None = None,
     only_conn_top: float | None = None,
     inflate: float | None = None,
     trim_off_wm: bool = False,
@@ -356,6 +368,8 @@ def v_3_droimaker(
             which to label specific GM ROIs after thresholding.
         volthr: Minimum size a cluster of voxels must have in order to remain a\
             GM ROI after thresholding. Can reduce 'noisy' clusters.
+        only_some_top: Restrict each found region to keep only N voxels with\
+            the highest inset values.
         only_conn_top: Select N max contiguous voxels in a region starting from\
             peak voxel and expanding.
         inflate: Number of voxels to pad each found ROI in order to turn GM\
@@ -392,6 +406,7 @@ def v_3_droimaker(
         prefix=prefix,
         refset=refset,
         volthr=volthr,
+        only_some_top=only_some_top,
         only_conn_top=only_conn_top,
         inflate=inflate,
         trim_off_wm=trim_off_wm,

niwrap_afni/afni/v_3d_afnito3_d.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO3_D_METADATA = Metadata(
-    id="51230e7f67f1e0eb607573872e1507d7fe45f41a.boutiques",
+    id="2e56ef52ac7f3be262fb2b8e920d983be907904e.boutiques",
     name="3dAFNIto3D",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,9 @@ V_3D_AFNITO3_D_METADATA = Metadata(
 V3dAfnito3DParameters = typing.TypedDict('V3dAfnito3DParameters', {
     "__STYX_TYPE__": typing.Literal["3dAFNIto3D"],
     "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "binary": bool,
+    "text": bool,
 })
 
 
@@ -57,25 +60,35 @@ class V3dAfnito3DOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    outfile: OutputPathType
+    outfile: OutputPathType | None
     """Output 3D file, either in binary or text format"""
 
 
 def v_3d_afnito3_d_params(
     dataset: InputPathType,
+    prefix: str | None = None,
+    binary: bool = False,
+    text: bool = False,
 ) -> V3dAfnito3DParameters:
     """
     Build parameters.
     
     Args:
         dataset: AFNI dataset to be converted.
+        prefix: Write result into file with specified prefix.
+        binary: Write data in binary format.
+        text: Write data in text format.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dAFNIto3D",
         "dataset": dataset,
+        "binary": binary,
+        "text": text,
     }
+    if prefix is not None:
+        params["prefix"] = prefix
     return params
 
 
@@ -94,8 +107,16 @@ def v_3d_afnito3_d_cargs(
     """
     cargs = []
     cargs.append("3dAFNIto3D")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("binary"):
+        cargs.append("-bin")
+    if params.get("text"):
+        cargs.append("-txt")
     return cargs
 
 
@@ -114,7 +135,7 @@ def v_3d_afnito3_d_outputs(
     """
     ret = V3dAfnito3DOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file("[PREFIX].3D"),
+        outfile=execution.output_file(params.get("prefix") + ".3D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
@@ -145,6 +166,9 @@ def v_3d_afnito3_d_execute(
 
 def v_3d_afnito3_d(
     dataset: InputPathType,
+    prefix: str | None = None,
+    binary: bool = False,
+    text: bool = False,
     runner: Runner | None = None,
 ) -> V3dAfnito3DOutputs:
     """
@@ -156,6 +180,9 @@ def v_3d_afnito3_d(
     
     Args:
         dataset: AFNI dataset to be converted.
+        prefix: Write result into file with specified prefix.
+        binary: Write data in binary format.
+        text: Write data in text format.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnito3DOutputs`).
@@ -164,6 +191,9 @@ def v_3d_afnito3_d(
     execution = runner.start_execution(V_3D_AFNITO3_D_METADATA)
     params = v_3d_afnito3_d_params(
         dataset=dataset,
+        prefix=prefix,
+        binary=binary,
+        text=text,
     )
     return v_3d_afnito3_d_execute(params, execution)