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

niwrap_afni/afni/v_3d_remlfit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_REMLFIT_METADATA = Metadata(
-    id="847ea79f5b61b9773e10438597e56d4e78c62c2e.boutiques",
+    id="9a5a03ff4aea32e95390547c4573b680ae1ca04b.boutiques",
     name="3dREMLfit",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -22,10 +22,14 @@ V3dRemlfitParameters = typing.TypedDict('V3dRemlfitParameters', {
     "temp_storage": bool,
     "mask": typing.NotRequired[InputPathType | None],
     "output_prefix": typing.NotRequired[str | None],
+    "no_fdr_curve": bool,
     "go_for_it": bool,
+    "max_a_param": typing.NotRequired[float | None],
     "max_b_param": typing.NotRequired[float | None],
     "grid_param": typing.NotRequired[float | None],
     "negative_corr": bool,
+    "quiet": bool,
+    "verbose": bool,
 })
 
 
@@ -89,10 +93,14 @@ def v_3d_remlfit_params(
     temp_storage: bool = False,
     mask: InputPathType | None = None,
     output_prefix: str | None = None,
+    no_fdr_curve: bool = False,
     go_for_it: bool = False,
+    max_a_param: float | None = None,
     max_b_param: float | None = None,
     grid_param: float | None = None,
     negative_corr: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
 ) -> V3dRemlfitParameters:
     """
     Build parameters.
@@ -111,11 +119,15 @@ def v_3d_remlfit_params(
         mask: Read dataset as a mask for the input; voxels outside the mask\
             will not be fit by the regression model.
         output_prefix: Dataset prefix for saving REML variance parameters.
+        no_fdr_curve: Do not add FDR curve data to bucket datasets.
         go_for_it: Force the program to continue past a failed collinearity\
             check.
+        max_a_param: Set max allowed AR a parameter.
         max_b_param: Set max allowed MA b parameter.
         grid_param: Set the number of grid divisions in the (a,b) grid.
         negative_corr: Allows negative correlations to be used.
+        quiet: Turn off most progress messages.
+        verbose: Turn on more progress messages.
     Returns:
         Parameter dictionary
     """
@@ -125,8 +137,11 @@ def v_3d_remlfit_params(
         "regression_matrix": regression_matrix,
         "sort_nods": sort_nods,
         "temp_storage": temp_storage,
+        "no_fdr_curve": no_fdr_curve,
         "go_for_it": go_for_it,
         "negative_corr": negative_corr,
+        "quiet": quiet,
+        "verbose": verbose,
     }
     if baseline_files is not None:
         params["baseline_files"] = baseline_files
@@ -134,6 +149,8 @@ def v_3d_remlfit_params(
         params["mask"] = mask
     if output_prefix is not None:
         params["output_prefix"] = output_prefix
+    if max_a_param is not None:
+        params["max_a_param"] = max_a_param
     if max_b_param is not None:
         params["max_b_param"] = max_b_param
     if grid_param is not None:
@@ -183,8 +200,15 @@ def v_3d_remlfit_cargs(
             "-Rvar",
             params.get("output_prefix")
         ])
+    if params.get("no_fdr_curve"):
+        cargs.append("-noFDR")
     if params.get("go_for_it"):
         cargs.append("-GOFORIT")
+    if params.get("max_a_param") is not None:
+        cargs.extend([
+            "-MAXa",
+            str(params.get("max_a_param"))
+        ])
     if params.get("max_b_param") is not None:
         cargs.extend([
             "-MAXb",
@@ -197,6 +221,10 @@ def v_3d_remlfit_cargs(
         ])
     if params.get("negative_corr"):
         cargs.append("-NEGcor")
+    if params.get("quiet"):
+        cargs.append("quiet")
+    if params.get("verbose"):
+        cargs.append("-verb")
     return cargs
 
 
@@ -258,10 +286,14 @@ def v_3d_remlfit(
     temp_storage: bool = False,
     mask: InputPathType | None = None,
     output_prefix: str | None = None,
+    no_fdr_curve: bool = False,
     go_for_it: bool = False,
+    max_a_param: float | None = None,
     max_b_param: float | None = None,
     grid_param: float | None = None,
     negative_corr: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
     runner: Runner | None = None,
 ) -> V3dRemlfitOutputs:
     """
@@ -286,11 +318,15 @@ def v_3d_remlfit(
         mask: Read dataset as a mask for the input; voxels outside the mask\
             will not be fit by the regression model.
         output_prefix: Dataset prefix for saving REML variance parameters.
+        no_fdr_curve: Do not add FDR curve data to bucket datasets.
         go_for_it: Force the program to continue past a failed collinearity\
             check.
+        max_a_param: Set max allowed AR a parameter.
         max_b_param: Set max allowed MA b parameter.
         grid_param: Set the number of grid divisions in the (a,b) grid.
         negative_corr: Allows negative correlations to be used.
+        quiet: Turn off most progress messages.
+        verbose: Turn on more progress messages.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRemlfitOutputs`).
@@ -305,10 +341,14 @@ def v_3d_remlfit(
         temp_storage=temp_storage,
         mask=mask,
         output_prefix=output_prefix,
+        no_fdr_curve=no_fdr_curve,
         go_for_it=go_for_it,
+        max_a_param=max_a_param,
         max_b_param=max_b_param,
         grid_param=grid_param,
         negative_corr=negative_corr,
+        quiet=quiet,
+        verbose=verbose,
     )
     return v_3d_remlfit_execute(params, execution)
 

niwrap_afni/afni/v_3d_roistats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ROISTATS_METADATA = Metadata(
-    id="80281254f3598a961619f69119f1d0eb9b58f421.boutiques",
+    id="b9c0ea474b143a895f00214ac150e218ee4b6ab6.boutiques",
     name="3dROIstats",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -192,7 +192,6 @@ def v_3d_roistats_cargs(
             "-mask",
             execution.input_file(params.get("mask"))
         ])
-    cargs.append("[OUT_FILE]")
     if params.get("debug"):
         cargs.append("-debug")
     if params.get("format1D"):

niwrap_afni/afni/v_3d_rsfc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RSFC_METADATA = Metadata(
-    id="b5c2a121f1ca24f0166e661caec651b36aec44bd.boutiques",
+    id="143254090adf81d94650422d3da0d7fcae499cc5.boutiques",
     name="3dRSFC",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,6 +18,27 @@ V3dRsfcParameters = typing.TypedDict('V3dRsfcParameters', {
     "fbot": float,
     "ftop": float,
     "input_dataset": InputPathType,
+    "despike": bool,
+    "ort_file": typing.NotRequired[InputPathType | None],
+    "dsort_file": typing.NotRequired[InputPathType | None],
+    "nodetrend": bool,
+    "time_step": typing.NotRequired[float | None],
+    "nfft": typing.NotRequired[int | None],
+    "norm": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "blur": typing.NotRequired[float | None],
+    "localpv": typing.NotRequired[float | None],
+    "input_alt": typing.NotRequired[InputPathType | None],
+    "band": typing.NotRequired[list[float] | None],
+    "prefix": typing.NotRequired[str | None],
+    "quiet": bool,
+    "no_rs_out": bool,
+    "un_bandpass_out": bool,
+    "no_rsfa": bool,
+    "bp_at_end": bool,
+    "notrans": bool,
+    "nosat": bool,
 })
 
 
@@ -59,9 +80,9 @@ class V3dRsfcOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    filtered_time_series: OutputPathType
+    filtered_time_series: OutputPathType | None
     """Filtered time series output"""
-    un_bandpassed_series: OutputPathType
+    un_bandpassed_series: OutputPathType | None
     """Un-bandpassed series output"""
 
 
@@ -69,6 +90,27 @@ def v_3d_rsfc_params(
     fbot: float,
     ftop: float,
     input_dataset: InputPathType,
+    despike: bool = False,
+    ort_file: InputPathType | None = None,
+    dsort_file: InputPathType | None = None,
+    nodetrend: bool = False,
+    time_step: float | None = None,
+    nfft: int | None = None,
+    norm: bool = False,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    blur: float | None = None,
+    localpv: float | None = None,
+    input_alt: InputPathType | None = None,
+    band: list[float] | None = None,
+    prefix: str | None = None,
+    quiet: bool = False,
+    no_rs_out: bool = False,
+    un_bandpass_out: bool = False,
+    no_rsfa: bool = False,
+    bp_at_end: bool = False,
+    notrans: bool = False,
+    nosat: bool = False,
 ) -> V3dRsfcParameters:
     """
     Build parameters.
@@ -77,6 +119,30 @@ def v_3d_rsfc_params(
         fbot: Lowest frequency in the passband, in Hz.
         ftop: Highest frequency in the passband (must be > fbot).
         input_dataset: Input dataset (3D+time sequence of volumes).
+        despike: Despike each time series before other processing.
+        ort_file: Also orthogonalize input to columns in specified file.
+        dsort_file: Orthogonalize each voxel to the corresponding voxel time\
+            series in specified dataset.
+        nodetrend: Skip the quadratic detrending of input before FFT-based\
+            bandpassing.
+        time_step: Set time step to specified value in seconds.
+        nfft: Set the FFT length to specified value.
+        norm: Make all output time series have L2 norm = 1.
+        mask: Specify mask dataset.
+        automask: Create a mask from the input dataset.
+        blur: Blur inside the mask only with specified FWHM in mm.
+        localpv: Replace each vector by the local Principal Vector from a\
+            neighborhood radius.
+        input_alt: Alternative way to specify input dataset.
+        band: Alternative way to specify passband frequencies.
+        prefix: Set prefix name of the output dataset.
+        quiet: Turn off the fun and informative messages.
+        no_rs_out: Don't output processed time series, just output parameters.
+        un_bandpass_out: Output the un-bandpassed series as well.
+        no_rsfa: Exclude RSFA output (default is to include).
+        bp_at_end: Bandpassing as the last step in the processing sequence.
+        notrans: Don't check for initial positive transients in the data.
+        nosat: Equivalent to -notrans, skips checking for initial transients.
     Returns:
         Parameter dictionary
     """
@@ -85,7 +151,38 @@ def v_3d_rsfc_params(
         "fbot": fbot,
         "ftop": ftop,
         "input_dataset": input_dataset,
+        "despike": despike,
+        "nodetrend": nodetrend,
+        "norm": norm,
+        "automask": automask,
+        "quiet": quiet,
+        "no_rs_out": no_rs_out,
+        "un_bandpass_out": un_bandpass_out,
+        "no_rsfa": no_rsfa,
+        "bp_at_end": bp_at_end,
+        "notrans": notrans,
+        "nosat": nosat,
     }
+    if ort_file is not None:
+        params["ort_file"] = ort_file
+    if dsort_file is not None:
+        params["dsort_file"] = dsort_file
+    if time_step is not None:
+        params["time_step"] = time_step
+    if nfft is not None:
+        params["nfft"] = nfft
+    if mask is not None:
+        params["mask"] = mask
+    if blur is not None:
+        params["blur"] = blur
+    if localpv is not None:
+        params["localpv"] = localpv
+    if input_alt is not None:
+        params["input_alt"] = input_alt
+    if band is not None:
+        params["band"] = band
+    if prefix is not None:
+        params["prefix"] = prefix
     return params
 
 
@@ -104,10 +201,81 @@ def v_3d_rsfc_cargs(
     """
     cargs = []
     cargs.append("3dRSFC")
-    cargs.append("[OPTIONS]")
     cargs.append(str(params.get("fbot")))
     cargs.append(str(params.get("ftop")))
     cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("despike"):
+        cargs.append("-despike")
+    if params.get("ort_file") is not None:
+        cargs.extend([
+            "-ort",
+            execution.input_file(params.get("ort_file"))
+        ])
+    if params.get("dsort_file") is not None:
+        cargs.extend([
+            "-dsort",
+            execution.input_file(params.get("dsort_file"))
+        ])
+    if params.get("nodetrend"):
+        cargs.append("-nodetrend")
+    if params.get("time_step") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("time_step"))
+        ])
+    if params.get("nfft") is not None:
+        cargs.extend([
+            "-nfft",
+            str(params.get("nfft"))
+        ])
+    if params.get("norm"):
+        cargs.append("-norm")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("blur") is not None:
+        cargs.extend([
+            "-blur",
+            str(params.get("blur"))
+        ])
+    if params.get("localpv") is not None:
+        cargs.extend([
+            "-localPV",
+            str(params.get("localpv"))
+        ])
+    if params.get("input_alt") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_alt"))
+        ])
+    if params.get("band") is not None:
+        cargs.extend([
+            "-band",
+            *map(str, params.get("band"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("no_rs_out"):
+        cargs.append("-no_rs_out")
+    if params.get("un_bandpass_out"):
+        cargs.append("-un_bp_out")
+    if params.get("no_rsfa"):
+        cargs.append("-no_rsfa")
+    if params.get("bp_at_end"):
+        cargs.append("-bp_at_end")
+    if params.get("notrans"):
+        cargs.append("-notrans")
+    if params.get("nosat"):
+        cargs.append("-nosat")
     return cargs
 
 
@@ -126,8 +294,8 @@ def v_3d_rsfc_outputs(
     """
     ret = V3dRsfcOutputs(
         root=execution.output_file("."),
-        filtered_time_series=execution.output_file("[PREFIX]_LFF+orig.*"),
-        un_bandpassed_series=execution.output_file("[PREFIX]_unBP+orig.*"),
+        filtered_time_series=execution.output_file(params.get("prefix") + "_LFF+orig.*") if (params.get("prefix") is not None) else None,
+        un_bandpassed_series=execution.output_file(params.get("prefix") + "_unBP+orig.*") if (params.get("prefix") is not None) else None,
     )
     return ret
 
@@ -161,6 +329,27 @@ def v_3d_rsfc(
     fbot: float,
     ftop: float,
     input_dataset: InputPathType,
+    despike: bool = False,
+    ort_file: InputPathType | None = None,
+    dsort_file: InputPathType | None = None,
+    nodetrend: bool = False,
+    time_step: float | None = None,
+    nfft: int | None = None,
+    norm: bool = False,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    blur: float | None = None,
+    localpv: float | None = None,
+    input_alt: InputPathType | None = None,
+    band: list[float] | None = None,
+    prefix: str | None = None,
+    quiet: bool = False,
+    no_rs_out: bool = False,
+    un_bandpass_out: bool = False,
+    no_rsfa: bool = False,
+    bp_at_end: bool = False,
+    notrans: bool = False,
+    nosat: bool = False,
     runner: Runner | None = None,
 ) -> V3dRsfcOutputs:
     """
@@ -175,6 +364,30 @@ def v_3d_rsfc(
         fbot: Lowest frequency in the passband, in Hz.
         ftop: Highest frequency in the passband (must be > fbot).
         input_dataset: Input dataset (3D+time sequence of volumes).
+        despike: Despike each time series before other processing.
+        ort_file: Also orthogonalize input to columns in specified file.
+        dsort_file: Orthogonalize each voxel to the corresponding voxel time\
+            series in specified dataset.
+        nodetrend: Skip the quadratic detrending of input before FFT-based\
+            bandpassing.
+        time_step: Set time step to specified value in seconds.
+        nfft: Set the FFT length to specified value.
+        norm: Make all output time series have L2 norm = 1.
+        mask: Specify mask dataset.
+        automask: Create a mask from the input dataset.
+        blur: Blur inside the mask only with specified FWHM in mm.
+        localpv: Replace each vector by the local Principal Vector from a\
+            neighborhood radius.
+        input_alt: Alternative way to specify input dataset.
+        band: Alternative way to specify passband frequencies.
+        prefix: Set prefix name of the output dataset.
+        quiet: Turn off the fun and informative messages.
+        no_rs_out: Don't output processed time series, just output parameters.
+        un_bandpass_out: Output the un-bandpassed series as well.
+        no_rsfa: Exclude RSFA output (default is to include).
+        bp_at_end: Bandpassing as the last step in the processing sequence.
+        notrans: Don't check for initial positive transients in the data.
+        nosat: Equivalent to -notrans, skips checking for initial transients.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRsfcOutputs`).
@@ -185,6 +398,27 @@ def v_3d_rsfc(
         fbot=fbot,
         ftop=ftop,
         input_dataset=input_dataset,
+        despike=despike,
+        ort_file=ort_file,
+        dsort_file=dsort_file,
+        nodetrend=nodetrend,
+        time_step=time_step,
+        nfft=nfft,
+        norm=norm,
+        mask=mask,
+        automask=automask,
+        blur=blur,
+        localpv=localpv,
+        input_alt=input_alt,
+        band=band,
+        prefix=prefix,
+        quiet=quiet,
+        no_rs_out=no_rs_out,
+        un_bandpass_out=un_bandpass_out,
+        no_rsfa=no_rsfa,
+        bp_at_end=bp_at_end,
+        notrans=notrans,
+        nosat=nosat,
     )
     return v_3d_rsfc_execute(params, execution)
 

niwrap_afni/afni/v_3d_stat_clust.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_STAT_CLUST_METADATA = Metadata(
-    id="fc722addfbc175c71d3a318d604f19ee64fdb599.boutiques",
+    id="284f4ab8bc45b6b47b8622cab065942bd38efb9a.boutiques",
     name="3dStatClust",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,6 +18,8 @@ V3dStatClustParameters = typing.TypedDict('V3dStatClustParameters', {
     "prefix": typing.NotRequired[str | None],
     "session_dir": typing.NotRequired[str | None],
     "verbose": bool,
+    "dist_euc": bool,
+    "dist_ind": bool,
     "dist_cor": bool,
     "thresh": str,
     "nclust": float,
@@ -76,6 +78,8 @@ def v_3d_stat_clust_params(
     prefix: str | None = None,
     session_dir: str | None = None,
     verbose: bool = False,
+    dist_euc: bool = False,
+    dist_ind: bool = False,
     dist_cor: bool = False,
 ) -> V3dStatClustParameters:
     """
@@ -92,6 +96,8 @@ def v_3d_stat_clust_params(
         prefix: Use 'pname' for the output dataset prefix name.
         session_dir: Use 'dir' for the output dataset session directory.
         verbose: Print out verbose output as the program proceeds.
+        dist_euc: Calculate Euclidean distance between parameters.
+        dist_ind: Statistical distance for independent parameters.
         dist_cor: Statistical distance for correlated parameters.
     Returns:
         Parameter dictionary
@@ -99,6 +105,8 @@ def v_3d_stat_clust_params(
     params = {
         "__STYXTYPE__": "3dStatClust",
         "verbose": verbose,
+        "dist_euc": dist_euc,
+        "dist_ind": dist_ind,
         "dist_cor": dist_cor,
         "thresh": thresh,
         "nclust": nclust,
@@ -138,6 +146,10 @@ def v_3d_stat_clust_cargs(
         ])
     if params.get("verbose"):
         cargs.append("-verb")
+    if params.get("dist_euc"):
+        cargs.append("-dist_euc")
+    if params.get("dist_ind"):
+        cargs.append("-dist_ind")
     if params.get("dist_cor"):
         cargs.append("-dist_cor")
     cargs.extend([
@@ -206,6 +218,8 @@ def v_3d_stat_clust(
     prefix: str | None = None,
     session_dir: str | None = None,
     verbose: bool = False,
+    dist_euc: bool = False,
+    dist_ind: bool = False,
     dist_cor: bool = False,
     runner: Runner | None = None,
 ) -> V3dStatClustOutputs:
@@ -229,6 +243,8 @@ def v_3d_stat_clust(
         prefix: Use 'pname' for the output dataset prefix name.
         session_dir: Use 'dir' for the output dataset session directory.
         verbose: Print out verbose output as the program proceeds.
+        dist_euc: Calculate Euclidean distance between parameters.
+        dist_ind: Statistical distance for independent parameters.
         dist_cor: Statistical distance for correlated parameters.
         runner: Command runner.
     Returns:
@@ -240,6 +256,8 @@ def v_3d_stat_clust(
         prefix=prefix,
         session_dir=session_dir,
         verbose=verbose,
+        dist_euc=dist_euc,
+        dist_ind=dist_ind,
         dist_cor=dist_cor,
         thresh=thresh,
         nclust=nclust,

niwrap_afni/afni/v_3d_tcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TCAT_METADATA = Metadata(
-    id="857f0c4b1d6c6ff7212eb0f219b0756a253e1817.boutiques",
+    id="023823c816c61a89ea1bb113572154f5901d616f.boutiques",
     name="3dTcat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,7 +17,9 @@ V3dTcatParameters = typing.TypedDict('V3dTcatParameters', {
     "__STYX_TYPE__": typing.Literal["3dTcat"],
     "rlt": typing.NotRequired[typing.Literal["", "+", "++"] | None],
     "in_files": InputPathType,
+    "out_file": typing.NotRequired[str | None],
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "num_threads": typing.NotRequired[int | None],
     "verbose": bool,
 })
 
@@ -62,14 +64,14 @@ class V3dTcatOutputs(typing.NamedTuple):
     """Output root folder. This is the root folder for all outputs."""
     out_file: OutputPathType
     """Output image file name."""
-    out_file_: OutputPathType
-    """Output file."""
 
 
 def v_3d_tcat_params(
     in_files: InputPathType,
     rlt: typing.Literal["", "+", "++"] | None = None,
+    out_file: str | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    num_threads: int | None = None,
     verbose: bool = False,
 ) -> V3dTcatParameters:
     """
@@ -82,7 +84,9 @@ def v_3d_tcat_params(
             least squares fit of 'a+b*t' to each voxel time series. option -rlt+\
             adds dataset mean back in. option -rlt++ adds overall mean of all\
             dataset timeseries back in.
+        out_file: Output image file name.
         outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        num_threads: Set number of threads.
         verbose: Print out some verbose output as the program.
     Returns:
         Parameter dictionary
@@ -94,8 +98,12 @@ def v_3d_tcat_params(
     }
     if rlt is not None:
         params["rlt"] = rlt
+    if out_file is not None:
+        params["out_file"] = out_file
     if outputtype is not None:
         params["outputtype"] = outputtype
+    if num_threads is not None:
+        params["num_threads"] = num_threads
     return params
 
 
@@ -119,9 +127,15 @@ def v_3d_tcat_cargs(
             "-rlt",
             params.get("rlt") + execution.input_file(params.get("in_files"))
         ])
-    cargs.append("[OUT_FILE]")
+    if params.get("out_file") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("out_file")
+        ])
     if params.get("outputtype") is not None:
         cargs.append(params.get("outputtype"))
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
     if params.get("verbose"):
         cargs.append("-verb")
     return cargs
@@ -143,7 +157,6 @@ def v_3d_tcat_outputs(
     ret = V3dTcatOutputs(
         root=execution.output_file("."),
         out_file=execution.output_file(pathlib.Path(params.get("in_files")).name + "_tcat"),
-        out_file_=execution.output_file("out_file"),
     )
     return ret
 
@@ -177,7 +190,9 @@ def v_3d_tcat_execute(
 def v_3d_tcat(
     in_files: InputPathType,
     rlt: typing.Literal["", "+", "++"] | None = None,
+    out_file: str | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    num_threads: int | None = None,
     verbose: bool = False,
     runner: Runner | None = None,
 ) -> V3dTcatOutputs:
@@ -197,7 +212,9 @@ def v_3d_tcat(
             least squares fit of 'a+b*t' to each voxel time series. option -rlt+\
             adds dataset mean back in. option -rlt++ adds overall mean of all\
             dataset timeseries back in.
+        out_file: Output image file name.
         outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        num_threads: Set number of threads.
         verbose: Print out some verbose output as the program.
         runner: Command runner.
     Returns:
@@ -208,7 +225,9 @@ def v_3d_tcat(
     params = v_3d_tcat_params(
         rlt=rlt,
         in_files=in_files,
+        out_file=out_file,
         outputtype=outputtype,
+        num_threads=num_threads,
         verbose=verbose,
     )
     return v_3d_tcat_execute(params, execution)

niwrap_afni/afni/v_3d_threeto_rgb.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_THREETO_RGB_METADATA = Metadata(
-    id="0e50efb1e4d4adac2b47669f62f58516c895a1cf.boutiques",
+    id="66d33991278e852be51fc79205b5a24fbb651ea3.boutiques",
     name="3dThreetoRGB",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -153,7 +153,6 @@ def v_3d_threeto_rgb_cargs(
     if params.get("anat"):
         cargs.append("-anat")
     cargs.append(execution.input_file(params.get("input_dataset")))
-    cargs.append("[DATASET1]")
     if params.get("input_dataset2") is not None:
         cargs.append(execution.input_file(params.get("input_dataset2")))
     if params.get("input_dataset3") is not None: