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

niwrap_afni/afni/v__compute_oc_weights.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__COMPUTE_OC_WEIGHTS_METADATA = Metadata(
-    id="4427220e56bd9be0b0fb6b294b7d2992dca6669c.boutiques",
+    id="ebfead8518bbfa4656b258644c98429751538187.boutiques",
     name="@compute_OC_weights",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,7 @@ V__COMPUTE_OC_WEIGHTS_METADATA = Metadata(
 VComputeOcWeightsParameters = typing.TypedDict('VComputeOcWeightsParameters', {
     "__STYX_TYPE__": typing.Literal["@compute_OC_weights"],
     "echo_times": typing.NotRequired[str | None],
+    "echo_times_file": typing.NotRequired[InputPathType | None],
     "echo_dsets": list[str],
     "prefix": typing.NotRequired[str | None],
     "def_to_equal": typing.NotRequired[str | None],
@@ -72,6 +73,7 @@ class VComputeOcWeightsOutputs(typing.NamedTuple):
 def v__compute_oc_weights_params(
     echo_dsets: list[str],
     echo_times: str | None = None,
+    echo_times_file: InputPathType | None = None,
     prefix: str | None = None,
     def_to_equal: str | None = None,
     oc_method: str | None = None,
@@ -87,6 +89,8 @@ def v__compute_oc_weights_params(
         echo_dsets: Specify one run of multi-echo EPI data.
         echo_times: Specify echo times as list (e.g., "15 30.5 41"). Use either\
             -echo_times or -echo_times_files.
+        echo_times_file: Specify file with echo times. Use either -echo_times\
+            or -echo_times_files.
         prefix: Specify prefix of resulting OC weights dataset (e.g.,\
             OC.weights.SUBJ).
         def_to_equal: Specify whether to default to equal weights (default =\
@@ -107,6 +111,8 @@ def v__compute_oc_weights_params(
     }
     if echo_times is not None:
         params["echo_times"] = echo_times
+    if echo_times_file is not None:
+        params["echo_times_file"] = echo_times_file
     if prefix is not None:
         params["prefix"] = prefix
     if def_to_equal is not None:
@@ -142,6 +148,11 @@ def v__compute_oc_weights_cargs(
             "-echo_times",
             params.get("echo_times")
         ])
+    if params.get("echo_times_file") is not None:
+        cargs.extend([
+            "-echo_times_file",
+            execution.input_file(params.get("echo_times_file"))
+        ])
     cargs.extend([
         "-echo_dsets",
         *params.get("echo_dsets")
@@ -228,6 +239,7 @@ def v__compute_oc_weights_execute(
 def v__compute_oc_weights(
     echo_dsets: list[str],
     echo_times: str | None = None,
+    echo_times_file: InputPathType | None = None,
     prefix: str | None = None,
     def_to_equal: str | None = None,
     oc_method: str | None = None,
@@ -248,6 +260,8 @@ def v__compute_oc_weights(
         echo_dsets: Specify one run of multi-echo EPI data.
         echo_times: Specify echo times as list (e.g., "15 30.5 41"). Use either\
             -echo_times or -echo_times_files.
+        echo_times_file: Specify file with echo times. Use either -echo_times\
+            or -echo_times_files.
         prefix: Specify prefix of resulting OC weights dataset (e.g.,\
             OC.weights.SUBJ).
         def_to_equal: Specify whether to default to equal weights (default =\
@@ -266,6 +280,7 @@ def v__compute_oc_weights(
     execution = runner.start_execution(V__COMPUTE_OC_WEIGHTS_METADATA)
     params = v__compute_oc_weights_params(
         echo_times=echo_times,
+        echo_times_file=echo_times_file,
         echo_dsets=echo_dsets,
         prefix=prefix,
         def_to_equal=def_to_equal,

niwrap_afni/afni/v__deblank_file_names.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__DEBLANK_FILE_NAMES_METADATA = Metadata(
-    id="da8da0abd18b50263679955b0ea74ae940b81571.boutiques",
+    id="68ddb73b60e7fe7159ec6fd9653bf2405c5c6592.boutiques",
     name="@DeblankFileNames",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -20,6 +20,7 @@ VDeblankFileNamesParameters = typing.TypedDict('VDeblankFileNamesParameters', {
     "demo_set": bool,
     "echo": bool,
     "help": bool,
+    "files": typing.NotRequired[list[InputPathType] | None],
 })
 
 
@@ -68,6 +69,7 @@ def v__deblank_file_names_params(
     demo_set: bool = False,
     echo: bool = False,
     help_: bool = False,
+    files: list[InputPathType] | None = None,
 ) -> VDeblankFileNamesParameters:
     """
     Build parameters.
@@ -78,6 +80,8 @@ def v__deblank_file_names_params(
         demo_set: Create a toy directory with bad names for testing.
         echo: Turn on script echo.
         help_: Display help message.
+        files: Specify files to fix as opposed to letting it fix all the names\
+            in the current directory.
     Returns:
         Parameter dictionary
     """
@@ -89,6 +93,8 @@ def v__deblank_file_names_params(
         "echo": echo,
         "help": help_,
     }
+    if files is not None:
+        params["files"] = files
     return params
 
 
@@ -117,7 +123,8 @@ def v__deblank_file_names_cargs(
         cargs.append("-echo")
     if params.get("help"):
         cargs.append("-help")
-    cargs.append("[FILES...]")
+    if params.get("files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("files")])
     return cargs
 
 
@@ -170,6 +177,7 @@ def v__deblank_file_names(
     demo_set: bool = False,
     echo: bool = False,
     help_: bool = False,
+    files: list[InputPathType] | None = None,
     runner: Runner | None = None,
 ) -> VDeblankFileNamesOutputs:
     """
@@ -185,6 +193,8 @@ def v__deblank_file_names(
         demo_set: Create a toy directory with bad names for testing.
         echo: Turn on script echo.
         help_: Display help message.
+        files: Specify files to fix as opposed to letting it fix all the names\
+            in the current directory.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VDeblankFileNamesOutputs`).
@@ -197,6 +207,7 @@ def v__deblank_file_names(
         demo_set=demo_set,
         echo=echo,
         help_=help_,
+        files=files,
     )
     return v__deblank_file_names_execute(params, execution)
 

niwrap_afni/afni/v__dice_metric.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__DICE_METRIC_METADATA = Metadata(
-    id="98eaa1a4d4837bef42b0135a72612d83719e6632.boutiques",
+    id="f304dc18b4f65735b81cfb996e5968c559cf2e3d.boutiques",
     name="@DiceMetric",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,8 +18,8 @@ VDiceMetricParameters = typing.TypedDict('VDiceMetricParameters', {
     "base": InputPathType,
     "dsets": list[InputPathType],
     "max_roi": typing.NotRequired[float | None],
+    "labeltable": typing.NotRequired[InputPathType | None],
     "forceoutput": typing.NotRequired[InputPathType | None],
-    "forceoutput_1": typing.NotRequired[InputPathType | None],
     "echo": bool,
     "save_match": bool,
     "save_diff": bool,
@@ -74,8 +74,8 @@ def v__dice_metric_params(
     base: InputPathType,
     dsets: list[InputPathType],
     max_roi: float | None = None,
+    labeltable: InputPathType | None = None,
     forceoutput: InputPathType | None = None,
-    forceoutput_1: InputPathType | None = None,
     echo: bool = False,
     save_match: bool = False,
     save_diff: bool = False,
@@ -94,8 +94,10 @@ def v__dice_metric_params(
             should be the last option on the command line.
         max_roi: The maximum possible ROI index. Default is 12 or based on\
             LTFILE if specified.
+        labeltable: If given, the labeltable is used to set the default MAX_ROI\
+            parameter. Also, this option forces an output for each key in the\
+            LTFILE.
         forceoutput: If given, force output for each class in LTFILE.
-        forceoutput_1: If given, force output for each class in LTFILE.
         echo: Set echo.
         save_match: Save volume showing BASE*equals(BASE,DSET).
         save_diff: Save volume showing BASE*(1-equals(BASE,DSET)).
@@ -126,10 +128,10 @@ def v__dice_metric_params(
     }
     if max_roi is not None:
         params["max_roi"] = max_roi
+    if labeltable is not None:
+        params["labeltable"] = labeltable
     if forceoutput is not None:
         params["forceoutput"] = forceoutput
-    if forceoutput_1 is not None:
-        params["forceoutput_1"] = forceoutput_1
     if prefix is not None:
         params["prefix"] = prefix
     return params
@@ -163,15 +165,15 @@ def v__dice_metric_cargs(
             "-max_N_roi",
             str(params.get("max_roi"))
         ])
-    if params.get("forceoutput") is not None:
+    if params.get("labeltable") is not None:
         cargs.extend([
-            "-forceoutput",
-            execution.input_file(params.get("forceoutput"))
+            "-labeltable",
+            execution.input_file(params.get("labeltable"))
         ])
-    if params.get("forceoutput_1") is not None:
+    if params.get("forceoutput") is not None:
         cargs.extend([
             "-forceoutput",
-            execution.input_file(params.get("forceoutput_1"))
+            execution.input_file(params.get("forceoutput"))
         ])
     if params.get("echo"):
         cargs.append("-echo")
@@ -242,8 +244,8 @@ def v__dice_metric(
     base: InputPathType,
     dsets: list[InputPathType],
     max_roi: float | None = None,
+    labeltable: InputPathType | None = None,
     forceoutput: InputPathType | None = None,
-    forceoutput_1: InputPathType | None = None,
     echo: bool = False,
     save_match: bool = False,
     save_diff: bool = False,
@@ -267,8 +269,10 @@ def v__dice_metric(
             should be the last option on the command line.
         max_roi: The maximum possible ROI index. Default is 12 or based on\
             LTFILE if specified.
+        labeltable: If given, the labeltable is used to set the default MAX_ROI\
+            parameter. Also, this option forces an output for each key in the\
+            LTFILE.
         forceoutput: If given, force output for each class in LTFILE.
-        forceoutput_1: If given, force output for each class in LTFILE.
         echo: Set echo.
         save_match: Save volume showing BASE*equals(BASE,DSET).
         save_diff: Save volume showing BASE*(1-equals(BASE,DSET)).
@@ -292,8 +296,8 @@ def v__dice_metric(
         base=base,
         dsets=dsets,
         max_roi=max_roi,
+        labeltable=labeltable,
         forceoutput=forceoutput,
-        forceoutput_1=forceoutput_1,
         echo=echo,
         save_match=save_match,
         save_diff=save_diff,

niwrap_afni/afni/v__djunct_edgy_align_check.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__DJUNCT_EDGY_ALIGN_CHECK_METADATA = Metadata(
-    id="b256b5bb4b47e9c6b85c30cb947f43710826ac49.boutiques",
+    id="8e479ed45f214bcb93f3842c5934b8e03c6fc47c.boutiques",
     name="@djunct_edgy_align_check",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -29,6 +29,15 @@ VDjunctEdgyAlignCheckParameters = typing.TypedDict('VDjunctEdgyAlignCheckParamet
     "monty": typing.NotRequired[float | None],
     "use_olay_grid": typing.NotRequired[str | None],
     "label_mode": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "ver_flag": bool,
+    "echo_flag": bool,
+    "sharpen_ulay_off_flag": bool,
+    "mask_olay_edges_flag": bool,
+    "no_cor_flag": bool,
+    "no_sag_flag": bool,
+    "no_axi_flag": bool,
+    "no_clean_flag": bool,
     "ulay_range": typing.NotRequired[list[float] | None],
     "ulay_range_nz": typing.NotRequired[list[float] | None],
     "ulay_range_am": typing.NotRequired[list[float] | None],
@@ -89,6 +98,15 @@ def v__djunct_edgy_align_check_params(
     monty: float | None = None,
     use_olay_grid: str | None = None,
     label_mode: str | None = None,
+    help_flag: bool = False,
+    ver_flag: bool = False,
+    echo_flag: bool = False,
+    sharpen_ulay_off_flag: bool = False,
+    mask_olay_edges_flag: bool = False,
+    no_cor_flag: bool = False,
+    no_sag_flag: bool = False,
+    no_axi_flag: bool = False,
+    no_clean_flag: bool = False,
     ulay_range: list[float] | None = None,
     ulay_range_nz: list[float] | None = None,
     ulay_range_am: list[float] | None = None,
@@ -111,6 +129,15 @@ def v__djunct_edgy_align_check_params(
         monty: Number of slices in Y-direction for montage.
         use_olay_grid: Grid interpolation method for overlay.
         label_mode: Mode for labeling.
+        help_flag: Display help message.
+        ver_flag: Show version.
+        echo_flag: Echo commands.
+        sharpen_ulay_off_flag: Disable underlay sharpening.
+        mask_olay_edges_flag: Mask overlay edges.
+        no_cor_flag: Exclude coronal plane.
+        no_sag_flag: Exclude sagittal plane.
+        no_axi_flag: Exclude axial plane.
+        no_clean_flag: Disable cleaning temporary files.
         ulay_range: Range for underlay {umin umax}.
         ulay_range_nz: Range for non-zero underlay {umin umax}.
         ulay_range_am: Range for auto-mask underlay {umin umax}.
@@ -122,6 +149,15 @@ def v__djunct_edgy_align_check_params(
         "ULAY": ulay,
         "OLAY": olay,
         "PREFIX": prefix,
+        "help_flag": help_flag,
+        "ver_flag": ver_flag,
+        "echo_flag": echo_flag,
+        "sharpen_ulay_off_flag": sharpen_ulay_off_flag,
+        "mask_olay_edges_flag": mask_olay_edges_flag,
+        "no_cor_flag": no_cor_flag,
+        "no_sag_flag": no_sag_flag,
+        "no_axi_flag": no_axi_flag,
+        "no_clean_flag": no_clean_flag,
     }
     if set_dicom_xyz is not None:
         params["set_dicom_xyz"] = set_dicom_xyz
@@ -194,15 +230,24 @@ def v__djunct_edgy_align_check_cargs(
         cargs.append(params.get("use_olay_grid"))
     if params.get("label_mode") is not None:
         cargs.append(params.get("label_mode"))
-    cargs.append("[help_flag]")
-    cargs.append("[ver_flag]")
-    cargs.append("[echo_flag]")
-    cargs.append("[sharpen_ulay_off_flag]")
-    cargs.append("[mask_olay_edges_flag]")
-    cargs.append("[no_cor_flag]")
-    cargs.append("[no_sag_flag]")
-    cargs.append("[no_axi_flag]")
-    cargs.append("[no_clean_flag]")
+    if params.get("help_flag"):
+        cargs.append("-help")
+    if params.get("ver_flag"):
+        cargs.append("-ver")
+    if params.get("echo_flag"):
+        cargs.append("-echo")
+    if params.get("sharpen_ulay_off_flag"):
+        cargs.append("-sharpen_ulay_off")
+    if params.get("mask_olay_edges_flag"):
+        cargs.append("-mask_olay_edges")
+    if params.get("no_cor_flag"):
+        cargs.append("-no_cor")
+    if params.get("no_sag_flag"):
+        cargs.append("-no_sag")
+    if params.get("no_axi_flag"):
+        cargs.append("-no_axi")
+    if params.get("no_clean_flag"):
+        cargs.append("-no_clean")
     if params.get("ulay_range") is not None:
         cargs.extend(map(str, params.get("ulay_range")))
     if params.get("ulay_range_nz") is not None:
@@ -271,6 +316,15 @@ def v__djunct_edgy_align_check(
     monty: float | None = None,
     use_olay_grid: str | None = None,
     label_mode: str | None = None,
+    help_flag: bool = False,
+    ver_flag: bool = False,
+    echo_flag: bool = False,
+    sharpen_ulay_off_flag: bool = False,
+    mask_olay_edges_flag: bool = False,
+    no_cor_flag: bool = False,
+    no_sag_flag: bool = False,
+    no_axi_flag: bool = False,
+    no_clean_flag: bool = False,
     ulay_range: list[float] | None = None,
     ulay_range_nz: list[float] | None = None,
     ulay_range_am: list[float] | None = None,
@@ -299,6 +353,15 @@ def v__djunct_edgy_align_check(
         monty: Number of slices in Y-direction for montage.
         use_olay_grid: Grid interpolation method for overlay.
         label_mode: Mode for labeling.
+        help_flag: Display help message.
+        ver_flag: Show version.
+        echo_flag: Echo commands.
+        sharpen_ulay_off_flag: Disable underlay sharpening.
+        mask_olay_edges_flag: Mask overlay edges.
+        no_cor_flag: Exclude coronal plane.
+        no_sag_flag: Exclude sagittal plane.
+        no_axi_flag: Exclude axial plane.
+        no_clean_flag: Disable cleaning temporary files.
         ulay_range: Range for underlay {umin umax}.
         ulay_range_nz: Range for non-zero underlay {umin umax}.
         ulay_range_am: Range for auto-mask underlay {umin umax}.
@@ -323,6 +386,15 @@ def v__djunct_edgy_align_check(
         monty=monty,
         use_olay_grid=use_olay_grid,
         label_mode=label_mode,
+        help_flag=help_flag,
+        ver_flag=ver_flag,
+        echo_flag=echo_flag,
+        sharpen_ulay_off_flag=sharpen_ulay_off_flag,
+        mask_olay_edges_flag=mask_olay_edges_flag,
+        no_cor_flag=no_cor_flag,
+        no_sag_flag=no_sag_flag,
+        no_axi_flag=no_axi_flag,
+        no_clean_flag=no_clean_flag,
         ulay_range=ulay_range,
         ulay_range_nz=ulay_range_nz,
         ulay_range_am=ulay_range_am,

niwrap_afni/afni/v__djunct_montage_coordinator.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__DJUNCT_MONTAGE_COORDINATOR_METADATA = Metadata(
-    id="9c2cbb473d95421a680be52f18d9f90f2ec86dfb.boutiques",
+    id="8d747f7169ee7e4179813dc1818309f1663d903c.boutiques",
     name="@djunct_montage_coordinator",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,6 +18,7 @@ VDjunctMontageCoordinatorParameters = typing.TypedDict('VDjunctMontageCoordinato
     "input_file": InputPathType,
     "montx": float,
     "monty": float,
+    "out_ijk": bool,
     "out_xyz": bool,
     "help": bool,
     "version": bool,
@@ -70,6 +71,7 @@ def v__djunct_montage_coordinator_params(
     input_file: InputPathType,
     montx: float,
     monty: float,
+    out_ijk: bool = False,
     out_xyz: bool = False,
     help_: bool = False,
     version: bool = False,
@@ -83,6 +85,7 @@ def v__djunct_montage_coordinator_params(
             of cols).
         monty: Montage dimension: number of panels along y-axis (i.e., number\
             of rows).
+        out_ijk: Make program output 'I J K' values.
         out_xyz: Make program output 'X Y Z' values.
         help_: See helpfile.
         version: See version number.
@@ -94,6 +97,7 @@ def v__djunct_montage_coordinator_params(
         "input_file": input_file,
         "montx": montx,
         "monty": monty,
+        "out_ijk": out_ijk,
         "out_xyz": out_xyz,
         "help": help_,
         "version": version,
@@ -128,6 +132,8 @@ def v__djunct_montage_coordinator_cargs(
         "-monty",
         str(params.get("monty"))
     ])
+    if params.get("out_ijk"):
+        cargs.append("-out_ijk")
     if params.get("out_xyz"):
         cargs.append("-out_xyz")
     if params.get("help"):
@@ -186,6 +192,7 @@ def v__djunct_montage_coordinator(
     input_file: InputPathType,
     montx: float,
     monty: float,
+    out_ijk: bool = False,
     out_xyz: bool = False,
     help_: bool = False,
     version: bool = False,
@@ -205,6 +212,7 @@ def v__djunct_montage_coordinator(
             of cols).
         monty: Montage dimension: number of panels along y-axis (i.e., number\
             of rows).
+        out_ijk: Make program output 'I J K' values.
         out_xyz: Make program output 'X Y Z' values.
         help_: See helpfile.
         version: See version number.
@@ -218,6 +226,7 @@ def v__djunct_montage_coordinator(
         input_file=input_file,
         montx=montx,
         monty=monty,
+        out_ijk=out_ijk,
         out_xyz=out_xyz,
         help_=help_,
         version=version,

niwrap_afni/afni/v__get_afni_res.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__GET_AFNI_RES_METADATA = Metadata(
-    id="8e9d3bd1817738927cfd2699a3bf4ffe4e305e07.boutiques",
+    id="e4786e6ad961f0208b6a0d65d657fb95dbacabc8.boutiques",
     name="@GetAfniRes",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -96,8 +96,9 @@ def v__get_afni_res_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("@GetAfniRes")
     if params.get("output_type") is not None:
-        cargs.append("@GetAfniRes" + params.get("output_type"))
+        cargs.append(params.get("output_type"))
     cargs.append(execution.input_file(params.get("input_dataset")))
     return cargs
 

niwrap_afni/afni/v__grad_flip_test.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__GRAD_FLIP_TEST_METADATA = Metadata(
-    id="83d02b240a4d1a85f3fc3038b96542312f180177.boutiques",
+    id="dda0017b4db56e4bd18047650c9ce39bfa2dacfb.boutiques",
     name="@GradFlipTest",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,10 +16,10 @@ V__GRAD_FLIP_TEST_METADATA = Metadata(
 VGradFlipTestParameters = typing.TypedDict('VGradFlipTestParameters', {
     "__STYX_TYPE__": typing.Literal["@GradFlipTest"],
     "dwi": InputPathType,
+    "grad_row_vec": typing.NotRequired[InputPathType | None],
+    "grad_col_vec": typing.NotRequired[InputPathType | None],
+    "grad_col_matA": typing.NotRequired[InputPathType | None],
     "grad_col_matT": typing.NotRequired[InputPathType | None],
-    "grad_col_matT_1": typing.NotRequired[InputPathType | None],
-    "grad_col_matT_2": typing.NotRequired[InputPathType | None],
-    "grad_col_matT_3": typing.NotRequired[InputPathType | None],
     "mask": typing.NotRequired[InputPathType | None],
     "bvals": typing.NotRequired[InputPathType | None],
     "thresh_fa": typing.NotRequired[float | None],
@@ -78,10 +78,10 @@ class VGradFlipTestOutputs(typing.NamedTuple):
 
 def v__grad_flip_test_params(
     dwi: InputPathType,
+    grad_row_vec: InputPathType | None = None,
+    grad_col_vec: InputPathType | None = None,
+    grad_col_mat_a: InputPathType | None = None,
     grad_col_mat_t: InputPathType | None = None,
-    grad_col_mat_t_1: InputPathType | None = None,
-    grad_col_mat_t_2: InputPathType | None = None,
-    grad_col_mat_t_3: InputPathType | None = None,
     mask: InputPathType | None = None,
     bvals: InputPathType | None = None,
     thresh_fa: float | None = None,
@@ -97,14 +97,12 @@ def v__grad_flip_test_params(
     
     Args:
         dwi: Set of DWIs (N total volumes).
+        grad_row_vec: Set of row-wise gradient vectors.
+        grad_col_vec: Set of column-wise gradient vectors.
+        grad_col_mat_a: Set of column-wise g- or b-matrix elements\
+            ("AFNI"-style format, "diagonal-first").
         grad_col_mat_t: Set of column-wise g- or b-matrix elements\
             ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_1: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_2: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_3: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
         mask: Optional mask (probably whole brain); otherwise, automasking is\
             performed.
         bvals: Can input bvals, if necessary (but shouldn't be necessary?).
@@ -127,14 +125,14 @@ def v__grad_flip_test_params(
         "scale_out_1000": scale_out_1000,
         "do_clean": do_clean,
     }
+    if grad_row_vec is not None:
+        params["grad_row_vec"] = grad_row_vec
+    if grad_col_vec is not None:
+        params["grad_col_vec"] = grad_col_vec
+    if grad_col_mat_a is not None:
+        params["grad_col_matA"] = grad_col_mat_a
     if grad_col_mat_t is not None:
         params["grad_col_matT"] = grad_col_mat_t
-    if grad_col_mat_t_1 is not None:
-        params["grad_col_matT_1"] = grad_col_mat_t_1
-    if grad_col_mat_t_2 is not None:
-        params["grad_col_matT_2"] = grad_col_mat_t_2
-    if grad_col_mat_t_3 is not None:
-        params["grad_col_matT_3"] = grad_col_mat_t_3
     if mask is not None:
         params["mask"] = mask
     if bvals is not None:
@@ -171,25 +169,25 @@ def v__grad_flip_test_cargs(
         "-in_dwi",
         execution.input_file(params.get("dwi"))
     ])
-    if params.get("grad_col_matT") is not None:
+    if params.get("grad_row_vec") is not None:
         cargs.extend([
-            "-in_col_matT",
-            execution.input_file(params.get("grad_col_matT"))
+            "-in_row_vec",
+            execution.input_file(params.get("grad_row_vec"))
         ])
-    if params.get("grad_col_matT_1") is not None:
+    if params.get("grad_col_vec") is not None:
         cargs.extend([
-            "-in_col_matT",
-            execution.input_file(params.get("grad_col_matT_1"))
+            "-in_col_vec",
+            execution.input_file(params.get("grad_col_vec"))
         ])
-    if params.get("grad_col_matT_2") is not None:
+    if params.get("grad_col_matA") is not None:
         cargs.extend([
-            "-in_col_matT",
-            execution.input_file(params.get("grad_col_matT_2"))
+            "-in_col_matA",
+            execution.input_file(params.get("grad_col_matA"))
         ])
-    if params.get("grad_col_matT_3") is not None:
+    if params.get("grad_col_matT") is not None:
         cargs.extend([
             "-in_col_matT",
-            execution.input_file(params.get("grad_col_matT_3"))
+            execution.input_file(params.get("grad_col_matT"))
         ])
     if params.get("mask") is not None:
         cargs.extend([
@@ -280,10 +278,10 @@ def v__grad_flip_test_execute(
 
 def v__grad_flip_test(
     dwi: InputPathType,
+    grad_row_vec: InputPathType | None = None,
+    grad_col_vec: InputPathType | None = None,
+    grad_col_mat_a: InputPathType | None = None,
     grad_col_mat_t: InputPathType | None = None,
-    grad_col_mat_t_1: InputPathType | None = None,
-    grad_col_mat_t_2: InputPathType | None = None,
-    grad_col_mat_t_3: InputPathType | None = None,
     mask: InputPathType | None = None,
     bvals: InputPathType | None = None,
     thresh_fa: float | None = None,
@@ -304,14 +302,12 @@ def v__grad_flip_test(
     
     Args:
         dwi: Set of DWIs (N total volumes).
+        grad_row_vec: Set of row-wise gradient vectors.
+        grad_col_vec: Set of column-wise gradient vectors.
+        grad_col_mat_a: Set of column-wise g- or b-matrix elements\
+            ("AFNI"-style format, "diagonal-first").
         grad_col_mat_t: Set of column-wise g- or b-matrix elements\
             ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_1: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_2: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
-        grad_col_mat_t_3: Set of column-wise g- or b-matrix elements\
-            ("TORTOISE"-style format, "row-first").
         mask: Optional mask (probably whole brain); otherwise, automasking is\
             performed.
         bvals: Can input bvals, if necessary (but shouldn't be necessary?).
@@ -333,10 +329,10 @@ def v__grad_flip_test(
     execution = runner.start_execution(V__GRAD_FLIP_TEST_METADATA)
     params = v__grad_flip_test_params(
         dwi=dwi,
+        grad_row_vec=grad_row_vec,
+        grad_col_vec=grad_col_vec,
+        grad_col_mat_a=grad_col_mat_a,
         grad_col_mat_t=grad_col_mat_t,
-        grad_col_mat_t_1=grad_col_mat_t_1,
-        grad_col_mat_t_2=grad_col_mat_t_2,
-        grad_col_mat_t_3=grad_col_mat_t_3,
         mask=mask,
         bvals=bvals,
         thresh_fa=thresh_fa,