niwrap-afni 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_afni/afni/convert_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONVERT_SURFACE_METADATA = Metadata(
-    id="2b7452b8bf057bc43ac7efc4c5a01abd5236749c.boutiques",
+    id="1515f74e677d72fcea38965b1c198adce4b27a82.boutiques",
     name="ConvertSurface",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,8 +19,11 @@ ConvertSurfaceParameters = typing.TypedDict('ConvertSurfaceParameters', {
     "output_surface": str,
     "surface_volume": typing.NotRequired[str | None],
     "transform_tlrc": bool,
+    "mni_rai": bool,
     "mni_lpi": bool,
+    "xmat_1D": typing.NotRequired[str | None],
     "ixmat_1D": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[str | None],
     "native": bool,
 })
 
@@ -72,8 +75,11 @@ def convert_surface_params(
     output_surface: str,
     surface_volume: str | None = None,
     transform_tlrc: bool = False,
+    mni_rai: bool = False,
     mni_lpi: bool = False,
+    xmat_1_d: str | None = None,
     ixmat_1_d: str | None = None,
+    seed: str | None = None,
     native: bool = False,
 ) -> ConvertSurfaceParameters:
     """
@@ -84,8 +90,12 @@ def convert_surface_params(
         output_surface: Specifies the output surface.
         surface_volume: Specifies a surface volume.
         transform_tlrc: Apply Talairach transform.
+        mni_rai: Turn AFNI tlrc coordinates (RAI) into MNI coord space in RAI.
         mni_lpi: Turn AFNI tlrc coordinates (RAI) into MNI coord space in LPI.
+        xmat_1_d: Apply transformation specified in 1D file.
         ixmat_1_d: Apply inverse transformation specified in 1D file.
+        seed: Specify SEED to seed the random number generator for random\
+            matrix generation.
         native: Write the output surface in the coordinate system native to its\
             format.
     Returns:
@@ -96,13 +106,18 @@ def convert_surface_params(
         "input_surface": input_surface,
         "output_surface": output_surface,
         "transform_tlrc": transform_tlrc,
+        "mni_rai": mni_rai,
         "mni_lpi": mni_lpi,
         "native": native,
     }
     if surface_volume is not None:
         params["surface_volume"] = surface_volume
+    if xmat_1_d is not None:
+        params["xmat_1D"] = xmat_1_d
     if ixmat_1_d is not None:
         params["ixmat_1D"] = ixmat_1_d
+    if seed is not None:
+        params["seed"] = seed
     return params
 
 
@@ -136,13 +151,25 @@ def convert_surface_cargs(
         ])
     if params.get("transform_tlrc"):
         cargs.append("-tlrc")
+    if params.get("mni_rai"):
+        cargs.append("-MNI_rai")
     if params.get("mni_lpi"):
         cargs.append("-MNI_lpi")
+    if params.get("xmat_1D") is not None:
+        cargs.extend([
+            "-xmat_1D",
+            params.get("xmat_1D")
+        ])
     if params.get("ixmat_1D") is not None:
         cargs.extend([
             "-ixmat_1D",
             params.get("ixmat_1D")
         ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            params.get("seed")
+        ])
     if params.get("native"):
         cargs.append("-native")
     return cargs
@@ -198,8 +225,11 @@ def convert_surface(
     output_surface: str,
     surface_volume: str | None = None,
     transform_tlrc: bool = False,
+    mni_rai: bool = False,
     mni_lpi: bool = False,
+    xmat_1_d: str | None = None,
     ixmat_1_d: str | None = None,
+    seed: str | None = None,
     native: bool = False,
     runner: Runner | None = None,
 ) -> ConvertSurfaceOutputs:
@@ -216,8 +246,12 @@ def convert_surface(
         output_surface: Specifies the output surface.
         surface_volume: Specifies a surface volume.
         transform_tlrc: Apply Talairach transform.
+        mni_rai: Turn AFNI tlrc coordinates (RAI) into MNI coord space in RAI.
         mni_lpi: Turn AFNI tlrc coordinates (RAI) into MNI coord space in LPI.
+        xmat_1_d: Apply transformation specified in 1D file.
         ixmat_1_d: Apply inverse transformation specified in 1D file.
+        seed: Specify SEED to seed the random number generator for random\
+            matrix generation.
         native: Write the output surface in the coordinate system native to its\
             format.
         runner: Command runner.
@@ -231,8 +265,11 @@ def convert_surface(
         output_surface=output_surface,
         surface_volume=surface_volume,
         transform_tlrc=transform_tlrc,
+        mni_rai=mni_rai,
         mni_lpi=mni_lpi,
+        xmat_1_d=xmat_1_d,
         ixmat_1_d=ixmat_1_d,
+        seed=seed,
         native=native,
     )
     return convert_surface_execute(params, execution)

niwrap_afni/afni/dicom_hinfo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_HINFO_METADATA = Metadata(
-    id="0de7df6566656068c4dc0dc5d6d2bae576cab754.boutiques",
+    id="f60ca8dfbe8adb47a80fe29002ccd4b8c68b8af2.boutiques",
     name="dicom_hinfo",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -20,6 +20,7 @@ DicomHinfoParameters = typing.TypedDict('DicomHinfoParameters', {
     "full_entry": bool,
     "no_name": bool,
     "namelast": bool,
+    "files": list[InputPathType],
 })
 
 
@@ -64,6 +65,7 @@ class DicomHinfoOutputs(typing.NamedTuple):
 
 def dicom_hinfo_params(
     tag: list[str],
+    files: list[InputPathType],
     sepstr: str | None = None,
     full_entry: bool = False,
     no_name: bool = False,
@@ -75,6 +77,7 @@ def dicom_hinfo_params(
     Args:
         tag: Specify one or more DICOM tags to print, in the format aaaa,bbbb\
             where aaaa and bbbb are hexadecimal digits.
+        files: DICOM file(s) to process.
         sepstr: Use the specified string to separate fields instead of space.
         full_entry: Output the full entry if it is more than one word or\
             contains white space.
@@ -89,6 +92,7 @@ def dicom_hinfo_params(
         "full_entry": full_entry,
         "no_name": no_name,
         "namelast": namelast,
+        "files": files,
     }
     if sepstr is not None:
         params["sepstr"] = sepstr
@@ -125,7 +129,7 @@ def dicom_hinfo_cargs(
         cargs.append("-no_name")
     if params.get("namelast"):
         cargs.append("-namelast")
-    cargs.append("[FILES...]")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
     return cargs
 
 
@@ -174,6 +178,7 @@ def dicom_hinfo_execute(
 
 def dicom_hinfo(
     tag: list[str],
+    files: list[InputPathType],
     sepstr: str | None = None,
     full_entry: bool = False,
     no_name: bool = False,
@@ -190,6 +195,7 @@ def dicom_hinfo(
     Args:
         tag: Specify one or more DICOM tags to print, in the format aaaa,bbbb\
             where aaaa and bbbb are hexadecimal digits.
+        files: DICOM file(s) to process.
         sepstr: Use the specified string to separate fields instead of space.
         full_entry: Output the full entry if it is more than one word or\
             contains white space.
@@ -207,6 +213,7 @@ def dicom_hinfo(
         full_entry=full_entry,
         no_name=no_name,
         namelast=namelast,
+        files=files,
     )
     return dicom_hinfo_execute(params, execution)
 

niwrap_afni/afni/dsetstat2p.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DSETSTAT2P_METADATA = Metadata(
-    id="b07011bb5bdd8084543d33f9a06e2ddf0d7fd9f2.boutiques",
+    id="7f3cbe6fcd6916e0065f078f2d35efc0d9307028.boutiques",
     name="dsetstat2p",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,8 @@ Dsetstat2pParameters = typing.TypedDict('Dsetstat2pParameters', {
     "__STYX_TYPE__": typing.Literal["dsetstat2p"],
     "dataset": str,
     "statval": float,
+    "bisided": bool,
+    "two_sided": bool,
     "one_sided": bool,
     "quiet": bool,
 })
@@ -67,6 +69,8 @@ class Dsetstat2pOutputs(typing.NamedTuple):
 def dsetstat2p_params(
     dataset: str,
     statval: float,
+    bisided: bool = False,
+    two_sided: bool = False,
     one_sided: bool = False,
     quiet: bool = False,
 ) -> Dsetstat2pParameters:
@@ -81,6 +85,8 @@ def dsetstat2p_params(
             of a string label selector.
         statval: Input stat-value S, which MUST be in the interval [0,\
             infinity).
+        bisided: Choose one-sided or bi-sided/two-sided testing.
+        two_sided: Choose one-sided or bi-sided/two-sided testing.
         one_sided: Choose one-sided or bi-sided/two-sided testing.
         quiet: An optional flag so that output ONLY the final statistic value\
             output to standard output; this can be then be viewed, redirected to a\
@@ -93,6 +99,8 @@ def dsetstat2p_params(
         "__STYXTYPE__": "dsetstat2p",
         "dataset": dataset,
         "statval": statval,
+        "bisided": bisided,
+        "two_sided": two_sided,
         "one_sided": one_sided,
         "quiet": quiet,
     }
@@ -116,6 +124,10 @@ def dsetstat2p_cargs(
     cargs.append("dsetstat2p")
     cargs.append(params.get("dataset"))
     cargs.append(str(params.get("statval")))
+    if params.get("bisided"):
+        cargs.append("-bisided")
+    if params.get("two_sided"):
+        cargs.append("-2sided")
     if params.get("one_sided"):
         cargs.append("-1sided")
     if params.get("quiet"):
@@ -170,6 +182,8 @@ def dsetstat2p_execute(
 def dsetstat2p(
     dataset: str,
     statval: float,
+    bisided: bool = False,
+    two_sided: bool = False,
     one_sided: bool = False,
     quiet: bool = False,
     runner: Runner | None = None,
@@ -189,6 +203,8 @@ def dsetstat2p(
             of a string label selector.
         statval: Input stat-value S, which MUST be in the interval [0,\
             infinity).
+        bisided: Choose one-sided or bi-sided/two-sided testing.
+        two_sided: Choose one-sided or bi-sided/two-sided testing.
         one_sided: Choose one-sided or bi-sided/two-sided testing.
         quiet: An optional flag so that output ONLY the final statistic value\
             output to standard output; this can be then be viewed, redirected to a\
@@ -203,6 +219,8 @@ def dsetstat2p(
     params = dsetstat2p_params(
         dataset=dataset,
         statval=statval,
+        bisided=bisided,
+        two_sided=two_sided,
         one_sided=one_sided,
         quiet=quiet,
     )

niwrap_afni/afni/fat_proc_align_anat_pair.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_ALIGN_ANAT_PAIR_METADATA = Metadata(
-    id="b81d41214e66c7f77b2bbc885c2f23369ad68254.boutiques",
+    id="bcbf8258d04aa65236dca0e8a04659e810e17311.boutiques",
     name="fat_proc_align_anat_pair",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,6 +19,7 @@ FatProcAlignAnatPairParameters = typing.TypedDict('FatProcAlignAnatPairParameter
     "input_t2w": InputPathType,
     "output_prefix": str,
     "output_grid": typing.NotRequired[float | None],
+    "out_t2w_grid": bool,
     "input_t2w_mask": typing.NotRequired[InputPathType | None],
     "do_ss_tmp_t1w": bool,
     "warp": typing.NotRequired[str | None],
@@ -80,6 +81,7 @@ def fat_proc_align_anat_pair_params(
     input_t2w: InputPathType,
     output_prefix: str,
     output_grid: float | None = None,
+    out_t2w_grid: bool = False,
     input_t2w_mask: InputPathType | None = None,
     do_ss_tmp_t1w: bool = False,
     warp: str | None = None,
@@ -96,6 +98,7 @@ def fat_proc_align_anat_pair_params(
         input_t2w: T2-weighted volume.
         output_prefix: Output prefix for files and snapshots.
         output_grid: Specify output T1w volume's final resolution (isotropic).
+        out_t2w_grid: Final T1w volume is on the T2W volume's grid.
         input_t2w_mask: Input a mask to apply to the T2w volume for alignment.
         do_ss_tmp_t1w: Apply skullstripping to the T1w volume during an\
             intermediate step.
@@ -114,6 +117,7 @@ def fat_proc_align_anat_pair_params(
         "input_t1w": input_t1w,
         "input_t2w": input_t2w,
         "output_prefix": output_prefix,
+        "out_t2w_grid": out_t2w_grid,
         "do_ss_tmp_t1w": do_ss_tmp_t1w,
         "no_cmd_out": no_cmd_out,
         "no_clean": no_clean,
@@ -163,6 +167,8 @@ def fat_proc_align_anat_pair_cargs(
             "-newgrid",
             str(params.get("output_grid"))
         ])
+    if params.get("out_t2w_grid"):
+        cargs.append("-out_t2w_grid")
     if params.get("input_t2w_mask") is not None:
         cargs.extend([
             "-in_t2w_mask",
@@ -244,6 +250,7 @@ def fat_proc_align_anat_pair(
     input_t2w: InputPathType,
     output_prefix: str,
     output_grid: float | None = None,
+    out_t2w_grid: bool = False,
     input_t2w_mask: InputPathType | None = None,
     do_ss_tmp_t1w: bool = False,
     warp: str | None = None,
@@ -266,6 +273,7 @@ def fat_proc_align_anat_pair(
         input_t2w: T2-weighted volume.
         output_prefix: Output prefix for files and snapshots.
         output_grid: Specify output T1w volume's final resolution (isotropic).
+        out_t2w_grid: Final T1w volume is on the T2W volume's grid.
         input_t2w_mask: Input a mask to apply to the T2w volume for alignment.
         do_ss_tmp_t1w: Apply skullstripping to the T1w volume during an\
             intermediate step.
@@ -287,6 +295,7 @@ def fat_proc_align_anat_pair(
         input_t2w=input_t2w,
         output_prefix=output_prefix,
         output_grid=output_grid,
+        out_t2w_grid=out_t2w_grid,
         input_t2w_mask=input_t2w_mask,
         do_ss_tmp_t1w=do_ss_tmp_t1w,
         warp=warp,

niwrap_afni/afni/fat_proc_convert_dcm_anat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_CONVERT_DCM_ANAT_METADATA = Metadata(
-    id="b710eae3e3dfce23951c6f5d44bae1dc65d2b536.boutiques",
+    id="9a696ac4933b9ed6358cfaf7a01ab13f371ba70a.boutiques",
     name="fat_proc_convert_dcm_anat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,7 @@ FAT_PROC_CONVERT_DCM_ANAT_METADATA = Metadata(
 
 FatProcConvertDcmAnatParameters = typing.TypedDict('FatProcConvertDcmAnatParameters', {
     "__STYX_TYPE__": typing.Literal["fat_proc_convert_dcm_anat"],
+    "dicom_directory": typing.NotRequired[str | None],
     "nifti_input": typing.NotRequired[InputPathType | None],
     "prefix": str,
     "workdir": typing.NotRequired[str | None],
@@ -71,6 +72,7 @@ class FatProcConvertDcmAnatOutputs(typing.NamedTuple):
 
 def fat_proc_convert_dcm_anat_params(
     prefix: str,
+    dicom_directory: str | None = None,
     nifti_input: InputPathType | None = None,
     workdir: str | None = None,
     orient: str | None = None,
@@ -85,6 +87,8 @@ def fat_proc_convert_dcm_anat_params(
     
     Args:
         prefix: Set prefix (and path) for output data.
+        dicom_directory: Input as DICOM directory; DIR_IN should contain only\
+            DICOM files; all will be selected.
         nifti_input: Input as NIFTI file (zipped or unzipped fine). Alternative\
             to '-indir ..'.
         workdir: Specify a working directory, which can be removed (default\
@@ -111,6 +115,8 @@ def fat_proc_convert_dcm_anat_params(
         "no_cmd_out": no_cmd_out,
         "no_qc_view": no_qc_view,
     }
+    if dicom_directory is not None:
+        params["dicom_directory"] = dicom_directory
     if nifti_input is not None:
         params["nifti_input"] = nifti_input
     if workdir is not None:
@@ -137,6 +143,11 @@ def fat_proc_convert_dcm_anat_cargs(
     """
     cargs = []
     cargs.append("fat_proc_convert_dcm_anat")
+    if params.get("dicom_directory") is not None:
+        cargs.extend([
+            "-indir",
+            params.get("dicom_directory")
+        ])
     if params.get("nifti_input") is not None:
         cargs.extend([
             "-innii",
@@ -219,6 +230,7 @@ def fat_proc_convert_dcm_anat_execute(
 
 def fat_proc_convert_dcm_anat(
     prefix: str,
+    dicom_directory: str | None = None,
     nifti_input: InputPathType | None = None,
     workdir: str | None = None,
     orient: str | None = None,
@@ -239,6 +251,8 @@ def fat_proc_convert_dcm_anat(
     
     Args:
         prefix: Set prefix (and path) for output data.
+        dicom_directory: Input as DICOM directory; DIR_IN should contain only\
+            DICOM files; all will be selected.
         nifti_input: Input as NIFTI file (zipped or unzipped fine). Alternative\
             to '-indir ..'.
         workdir: Specify a working directory, which can be removed (default\
@@ -261,6 +275,7 @@ def fat_proc_convert_dcm_anat(
     runner = runner or get_global_runner()
     execution = runner.start_execution(FAT_PROC_CONVERT_DCM_ANAT_METADATA)
     params = fat_proc_convert_dcm_anat_params(
+        dicom_directory=dicom_directory,
         nifti_input=nifti_input,
         prefix=prefix,
         workdir=workdir,

niwrap_afni/afni/fat_roi_row.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_ROI_ROW_METADATA = Metadata(
-    id="027b80948cf0bd1ac046353e98ebb2ca04186002.boutiques",
+    id="a4a1c061c97d682d3d4d61503f3c28a11502fc06.boutiques",
     name="fat_roi_row",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -119,19 +119,16 @@ def fat_roi_row_cargs(
         "-r",
         params.get("roi")
     ])
-    cargs.append("{")
     if params.get("matrix_files") is not None:
         cargs.extend([
             "-m",
             params.get("matrix_files")
         ])
-    cargs.append("|")
     if params.get("list_file") is not None:
         cargs.extend([
             "-l",
             execution.input_file(params.get("list_file"))
         ])
-    cargs.append("}")
     if params.get("extern_labs_no"):
         cargs.append("-E")
     return cargs

niwrap_afni/afni/fsread_annot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSREAD_ANNOT_METADATA = Metadata(
-    id="1aee44cf7efa00cb2630f7f3d7fb84af69eadb4f.boutiques",
+    id="791089bdafa5aacda0d88f6366afe5d004fd749e.boutiques",
     name="FSread_annot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -155,7 +155,7 @@ def fsread_annot_cargs(
     cargs.append("FSread_annot")
     cargs.extend([
         "-input",
-        "-" + execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile"))
     ])
     if params.get("hemi") is not None:
         cargs.extend([

niwrap_afni/afni/imrotate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMROTATE_METADATA = Metadata(
-    id="046eb12264816ed4b6d2246d2d697caf596e0670.boutiques",
+    id="7c817965f8c449aac8c4bfbde437361551c5546b.boutiques",
     name="imrotate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,7 @@ IMROTATE_METADATA = Metadata(
 
 ImrotateParameters = typing.TypedDict('ImrotateParameters', {
     "__STYX_TYPE__": typing.Literal["imrotate"],
+    "linear_interpolation": bool,
     "fourier_interpolation": bool,
     "dx": float,
     "dy": float,
@@ -72,6 +73,7 @@ def imrotate_params(
     phi: float,
     input_image: InputPathType,
     output_image: str,
+    linear_interpolation: bool = False,
     fourier_interpolation: bool = False,
 ) -> ImrotateParameters:
     """
@@ -83,12 +85,14 @@ def imrotate_params(
         phi: Degrees to rotate clockwise.
         input_image: Input image file.
         output_image: Output image file.
+        linear_interpolation: Use bilinear interpolation (default is bicubic).
         fourier_interpolation: Use Fourier interpolation.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "imrotate",
+        "linear_interpolation": linear_interpolation,
         "fourier_interpolation": fourier_interpolation,
         "dx": dx,
         "dy": dy,
@@ -114,6 +118,8 @@ def imrotate_cargs(
     """
     cargs = []
     cargs.append("imrotate")
+    if params.get("linear_interpolation"):
+        cargs.append("-linear")
     if params.get("fourier_interpolation"):
         cargs.append("-Fourier")
     cargs.append(str(params.get("dx")))
@@ -174,6 +180,7 @@ def imrotate(
     phi: float,
     input_image: InputPathType,
     output_image: str,
+    linear_interpolation: bool = False,
     fourier_interpolation: bool = False,
     runner: Runner | None = None,
 ) -> ImrotateOutputs:
@@ -190,6 +197,7 @@ def imrotate(
         phi: Degrees to rotate clockwise.
         input_image: Input image file.
         output_image: Output image file.
+        linear_interpolation: Use bilinear interpolation (default is bicubic).
         fourier_interpolation: Use Fourier interpolation.
         runner: Command runner.
     Returns:
@@ -198,6 +206,7 @@ def imrotate(
     runner = runner or get_global_runner()
     execution = runner.start_execution(IMROTATE_METADATA)
     params = imrotate_params(
+        linear_interpolation=linear_interpolation,
         fourier_interpolation=fourier_interpolation,
         dx=dx,
         dy=dy,

niwrap_afni/afni/myget.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MYGET_METADATA = Metadata(
-    id="2f6d3f9ad29fa84e230f411a821134ff68c91853.boutiques",
+    id="10043a869267d2f44f577e75349933f7e7bb0e5e.boutiques",
     name="myget",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,7 @@ MygetParameters = typing.TypedDict('MygetParameters', {
     "__STYX_TYPE__": typing.Literal["myget"],
     "protocol_version": typing.NotRequired[typing.Literal["-1", "-1.1"] | None],
     "url": str,
+    "output_file": str,
 })
 
 
@@ -64,6 +65,7 @@ class MygetOutputs(typing.NamedTuple):
 
 def myget_params(
     url: str,
+    output_file: str,
     protocol_version: typing.Literal["-1", "-1.1"] | None = None,
 ) -> MygetParameters:
     """
@@ -71,6 +73,7 @@ def myget_params(
     
     Args:
         url: The URL to download the file from.
+        output_file: The filename to save the downloaded file.
         protocol_version: Specify protocol version. You can choose between -1\
             or -1.1.
     Returns:
@@ -79,6 +82,7 @@ def myget_params(
     params = {
         "__STYXTYPE__": "myget",
         "url": url,
+        "output_file": output_file,
     }
     if protocol_version is not None:
         params["protocol_version"] = protocol_version
@@ -99,8 +103,14 @@ def myget_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("myget")
     if params.get("protocol_version") is not None:
-        cargs.append("myget" + params.get("protocol_version") + params.get("url"))
+        cargs.append(params.get("protocol_version"))
+    cargs.append(params.get("url"))
+    cargs.extend([
+        ">",
+        params.get("output_file")
+    ])
     return cargs
 
 
@@ -119,7 +129,7 @@ def myget_outputs(
     """
     ret = MygetOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("[OUTPUT_FILE]"),
+        output_file=execution.output_file(params.get("output_file")),
     )
     return ret
 
@@ -150,6 +160,7 @@ def myget_execute(
 
 def myget(
     url: str,
+    output_file: str,
     protocol_version: typing.Literal["-1", "-1.1"] | None = None,
     runner: Runner | None = None,
 ) -> MygetOutputs:
@@ -162,6 +173,7 @@ def myget(
     
     Args:
         url: The URL to download the file from.
+        output_file: The filename to save the downloaded file.
         protocol_version: Specify protocol version. You can choose between -1\
             or -1.1.
         runner: Command runner.
@@ -173,6 +185,7 @@ def myget(
     params = myget_params(
         protocol_version=protocol_version,
         url=url,
+        output_file=output_file,
     )
     return myget_execute(params, execution)
 

niwrap_afni/afni/nifti_tool.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NIFTI_TOOL_METADATA = Metadata(
-    id="3d62871ad5a6df5a56027e145232bf726b83d960.boutiques",
+    id="38a2d9449adee7d6233168e977d87d95385ebe37.boutiques",
     name="nifti_tool",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -146,7 +146,8 @@ def nifti_tool_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("nifti_tool" + params.get("action"))
+    cargs.append("nifti_tool")
+    cargs.append(params.get("action"))
     if params.get("input_files") is not None:
         cargs.extend([
             "-infiles",