niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/run_segment_subject_t1_auto_estimate_alveus_ml_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
-    id="4f9a46fb43606ac0251e70e49508d55ff638b63c.boutiques",
+    id="757d63d26afce0f743109efcef0de951a08acf10.boutiques",
     name="run_segmentSubjectT1_autoEstimateAlveusML.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
 
 
 RunSegmentSubjectT1AutoEstimateAlveusMlShParameters = typing.TypedDict('RunSegmentSubjectT1AutoEstimateAlveusMlShParameters', {
-    "__STYXTYPE__": typing.Literal["run_segmentSubjectT1_autoEstimateAlveusML.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_segmentSubjectT1_autoEstimateAlveusML.sh"]],
+    "deployed_mcr_root": str,
+    "additional_args": typing.NotRequired[str | None],
+})
+RunSegmentSubjectT1AutoEstimateAlveusMlShParametersTagged = typing.TypedDict('RunSegmentSubjectT1AutoEstimateAlveusMlShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_segmentSubjectT1_autoEstimateAlveusML.sh"],
     "deployed_mcr_root": str,
     "additional_args": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "run_segmentSubjectT1_autoEstimateAlveusML.sh": run_segment_subject_t1_auto_estimate_alveus_ml_sh_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_subject_t1_auto_estimate_alveus_ml_sh(...)`.
+    Output object returned when calling `RunSegmentSubjectT1AutoEstimateAlveusMlShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
 def run_segment_subject_t1_auto_estimate_alveus_ml_sh_params(
     deployed_mcr_root: str,
     additional_args: str | None = None,
-) -> RunSegmentSubjectT1AutoEstimateAlveusMlShParameters:
+) -> RunSegmentSubjectT1AutoEstimateAlveusMlShParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_segmentSubjectT1_autoEstimateAlveusML.sh",
+        "@type": "freesurfer/run_segmentSubjectT1_autoEstimateAlveusML.sh",
         "deployed_mcr_root": deployed_mcr_root,
     }
     if additional_args is not None:
@@ -96,9 +70,9 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh_cargs(
     """
     cargs = []
     cargs.append("run_segmentSubjectT1_autoEstimateAlveusML.sh")
-    cargs.append(params.get("deployed_mcr_root"))
-    if params.get("additional_args") is not None:
-        cargs.append(params.get("additional_args"))
+    cargs.append(params.get("deployed_mcr_root", None))
+    if params.get("additional_args", None) is not None:
+        cargs.append(params.get("additional_args", None))
     return cargs
 
 
@@ -123,11 +97,13 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh_outputs(
 
 def run_segment_subject_t1_auto_estimate_alveus_ml_sh_execute(
     params: RunSegmentSubjectT1AutoEstimateAlveusMlShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs:
     """
-    A script to automatically estimate Alveus using machine learning with the given
-    subject T1 image.
+    run_segmentSubjectT1_autoEstimateAlveusML.sh
+    
+    A script to automatically estimate Alveus using machine learning with the
+    given subject T1 image.
     
     Author: FreeSurfer Developers
     
@@ -135,10 +111,12 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_subject_t1_auto_estimate_alveus_ml_sh_cargs(params, execution)
     ret = run_segment_subject_t1_auto_estimate_alveus_ml_sh_outputs(params, execution)
@@ -152,8 +130,10 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh(
     runner: Runner | None = None,
 ) -> RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs:
     """
-    A script to automatically estimate Alveus using machine learning with the given
-    subject T1 image.
+    run_segmentSubjectT1_autoEstimateAlveusML.sh
+    
+    A script to automatically estimate Alveus using machine learning with the
+    given subject T1 image.
     
     Author: FreeSurfer Developers
     
@@ -166,19 +146,17 @@ def run_segment_subject_t1_auto_estimate_alveus_ml_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = run_segment_subject_t1_auto_estimate_alveus_ml_sh_params(
         deployed_mcr_root=deployed_mcr_root,
         additional_args=additional_args,
     )
-    return run_segment_subject_t1_auto_estimate_alveus_ml_sh_execute(params, execution)
+    return run_segment_subject_t1_auto_estimate_alveus_ml_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA",
     "RunSegmentSubjectT1AutoEstimateAlveusMlShOutputs",
-    "RunSegmentSubjectT1AutoEstimateAlveusMlShParameters",
     "run_segment_subject_t1_auto_estimate_alveus_ml_sh",
+    "run_segment_subject_t1_auto_estimate_alveus_ml_sh_execute",
     "run_segment_subject_t1_auto_estimate_alveus_ml_sh_params",
 ]

niwrap_freesurfer/freesurfer/run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
-    id="bf2051c733cf330a51f7a8fb68683e56389c2d7f.boutiques",
+    id="0039b4cbbcd262f2ed90f5eb700b50fa19f38118.boutiques",
     name="run_segmentSubjectT1T2_autoEstimateAlveusML.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
 
 
 RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters = typing.TypedDict('RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters', {
-    "__STYXTYPE__": typing.Literal["run_segmentSubjectT1T2_autoEstimateAlveusML.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_segmentSubjectT1T2_autoEstimateAlveusML.sh"]],
+    "deployed_mcr_root": str,
+    "additional_args": typing.NotRequired[str | None],
+})
+RunSegmentSubjectT1T2AutoEstimateAlveusMlShParametersTagged = typing.TypedDict('RunSegmentSubjectT1T2AutoEstimateAlveusMlShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_segmentSubjectT1T2_autoEstimateAlveusML.sh"],
     "deployed_mcr_root": str,
     "additional_args": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "run_segmentSubjectT1T2_autoEstimateAlveusML.sh": run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh(...)`.
+    Output object returned when calling `RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
 def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_params(
     deployed_mcr_root: str,
     additional_args: str | None = None,
-) -> RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters:
+) -> RunSegmentSubjectT1T2AutoEstimateAlveusMlShParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +49,7 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_segmentSubjectT1T2_autoEstimateAlveusML.sh",
+        "@type": "freesurfer/run_segmentSubjectT1T2_autoEstimateAlveusML.sh",
         "deployed_mcr_root": deployed_mcr_root,
     }
     if additional_args is not None:
@@ -98,9 +72,9 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_cargs(
     """
     cargs = []
     cargs.append("run_segmentSubjectT1T2_autoEstimateAlveusML.sh")
-    cargs.append(params.get("deployed_mcr_root"))
-    if params.get("additional_args") is not None:
-        cargs.append(params.get("additional_args"))
+    cargs.append(params.get("deployed_mcr_root", None))
+    if params.get("additional_args", None) is not None:
+        cargs.append(params.get("additional_args", None))
     return cargs
 
 
@@ -125,9 +99,11 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_outputs(
 
 def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_execute(
     params: RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs:
     """
+    run_segmentSubjectT1T2_autoEstimateAlveusML.sh
+    
     Automated segmentation tool for T1 and T2 weighted images to estimate the
     Alveus.
     
@@ -137,10 +113,12 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_cargs(params, execution)
     ret = run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_outputs(params, execution)
@@ -154,6 +132,8 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh(
     runner: Runner | None = None,
 ) -> RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs:
     """
+    run_segmentSubjectT1T2_autoEstimateAlveusML.sh
+    
     Automated segmentation tool for T1 and T2 weighted images to estimate the
     Alveus.
     
@@ -170,19 +150,17 @@ def run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_params(
         deployed_mcr_root=deployed_mcr_root,
         additional_args=additional_args,
     )
-    return run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_execute(params, execution)
+    return run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA",
     "RunSegmentSubjectT1T2AutoEstimateAlveusMlShOutputs",
-    "RunSegmentSubjectT1T2AutoEstimateAlveusMlShParameters",
     "run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh",
+    "run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_execute",
     "run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh_params",
 ]

niwrap_freesurfer/freesurfer/run_segment_subject_t2_auto_estimate_alveus_ml_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
-    id="2a8c1490dc550d5a8ebdcd5a722be9a6d0cb534c.boutiques",
+    id="b0e9bb93430b7223bae3be950c78c1f580f9abba.boutiques",
     name="run_segmentSubjectT2_autoEstimateAlveusML.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA = Metadata(
 
 
 RunSegmentSubjectT2AutoEstimateAlveusMlShParameters = typing.TypedDict('RunSegmentSubjectT2AutoEstimateAlveusMlShParameters', {
-    "__STYXTYPE__": typing.Literal["run_segmentSubjectT2_autoEstimateAlveusML.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_segmentSubjectT2_autoEstimateAlveusML.sh"]],
+    "deployed_mcr_root": str,
+    "arguments": typing.NotRequired[list[str] | None],
+})
+RunSegmentSubjectT2AutoEstimateAlveusMlShParametersTagged = typing.TypedDict('RunSegmentSubjectT2AutoEstimateAlveusMlShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_segmentSubjectT2_autoEstimateAlveusML.sh"],
     "deployed_mcr_root": str,
     "arguments": typing.NotRequired[list[str] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "run_segmentSubjectT2_autoEstimateAlveusML.sh": run_segment_subject_t2_auto_estimate_alveus_ml_sh_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_subject_t2_auto_estimate_alveus_ml_sh(...)`.
+    Output object returned when calling `RunSegmentSubjectT2AutoEstimateAlveusMlShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs(typing.NamedTuple):
 def run_segment_subject_t2_auto_estimate_alveus_ml_sh_params(
     deployed_mcr_root: str,
     arguments: list[str] | None = None,
-) -> RunSegmentSubjectT2AutoEstimateAlveusMlShParameters:
+) -> RunSegmentSubjectT2AutoEstimateAlveusMlShParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +49,7 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_segmentSubjectT2_autoEstimateAlveusML.sh",
+        "@type": "freesurfer/run_segmentSubjectT2_autoEstimateAlveusML.sh",
         "deployed_mcr_root": deployed_mcr_root,
     }
     if arguments is not None:
@@ -98,9 +72,9 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh_cargs(
     """
     cargs = []
     cargs.append("run_segmentSubjectT2_autoEstimateAlveusML.sh")
-    cargs.append(params.get("deployed_mcr_root"))
-    if params.get("arguments") is not None:
-        cargs.extend(params.get("arguments"))
+    cargs.append(params.get("deployed_mcr_root", None))
+    if params.get("arguments", None) is not None:
+        cargs.extend(params.get("arguments", None))
     return cargs
 
 
@@ -125,9 +99,11 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh_outputs(
 
 def run_segment_subject_t2_auto_estimate_alveus_ml_sh_execute(
     params: RunSegmentSubjectT2AutoEstimateAlveusMlShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs:
     """
+    run_segmentSubjectT2_autoEstimateAlveusML.sh
+    
     Script to run segmentSubjectT2_autoEstimateAlveusML operation. This script
     requires a MATLAB Compiler Runtime (MCR) root directory as input, but help
     output indicates missing library reference for operation.
@@ -138,10 +114,12 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_subject_t2_auto_estimate_alveus_ml_sh_cargs(params, execution)
     ret = run_segment_subject_t2_auto_estimate_alveus_ml_sh_outputs(params, execution)
@@ -155,6 +133,8 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh(
     runner: Runner | None = None,
 ) -> RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs:
     """
+    run_segmentSubjectT2_autoEstimateAlveusML.sh
+    
     Script to run segmentSubjectT2_autoEstimateAlveusML operation. This script
     requires a MATLAB Compiler Runtime (MCR) root directory as input, but help
     output indicates missing library reference for operation.
@@ -172,19 +152,17 @@ def run_segment_subject_t2_auto_estimate_alveus_ml_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA)
     params = run_segment_subject_t2_auto_estimate_alveus_ml_sh_params(
         deployed_mcr_root=deployed_mcr_root,
         arguments=arguments,
     )
-    return run_segment_subject_t2_auto_estimate_alveus_ml_sh_execute(params, execution)
+    return run_segment_subject_t2_auto_estimate_alveus_ml_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_SH_METADATA",
     "RunSegmentSubjectT2AutoEstimateAlveusMlShOutputs",
-    "RunSegmentSubjectT2AutoEstimateAlveusMlShParameters",
     "run_segment_subject_t2_auto_estimate_alveus_ml_sh",
+    "run_segment_subject_t2_auto_estimate_alveus_ml_sh_execute",
     "run_segment_subject_t2_auto_estimate_alveus_ml_sh_params",
 ]

niwrap_freesurfer/freesurfer/run_segment_thalamic_nuclei_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_THALAMIC_NUCLEI_SH_METADATA = Metadata(
-    id="58c7623548d514cfc3a6445924c9c49471329b52.boutiques",
+    id="2ed331f31f1f7dea89ed1592528e5062490dfb4e.boutiques",
     name="run_SegmentThalamicNuclei.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_SEGMENT_THALAMIC_NUCLEI_SH_METADATA = Metadata(
 
 
 RunSegmentThalamicNucleiShParameters = typing.TypedDict('RunSegmentThalamicNucleiShParameters', {
-    "__STYXTYPE__": typing.Literal["run_SegmentThalamicNuclei.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_SegmentThalamicNuclei.sh"]],
+    "mcr_root": str,
+    "args": typing.NotRequired[list[str] | None],
+})
+RunSegmentThalamicNucleiShParametersTagged = typing.TypedDict('RunSegmentThalamicNucleiShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_SegmentThalamicNuclei.sh"],
     "mcr_root": str,
     "args": typing.NotRequired[list[str] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "run_SegmentThalamicNuclei.sh": run_segment_thalamic_nuclei_sh_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class RunSegmentThalamicNucleiShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_thalamic_nuclei_sh(...)`.
+    Output object returned when calling `RunSegmentThalamicNucleiShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunSegmentThalamicNucleiShOutputs(typing.NamedTuple):
 def run_segment_thalamic_nuclei_sh_params(
     mcr_root: str,
     args: list[str] | None = None,
-) -> RunSegmentThalamicNucleiShParameters:
+) -> RunSegmentThalamicNucleiShParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def run_segment_thalamic_nuclei_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_SegmentThalamicNuclei.sh",
+        "@type": "freesurfer/run_SegmentThalamicNuclei.sh",
         "mcr_root": mcr_root,
     }
     if args is not None:
@@ -97,9 +71,9 @@ def run_segment_thalamic_nuclei_sh_cargs(
     """
     cargs = []
     cargs.append("run_SegmentThalamicNuclei.sh")
-    cargs.append(params.get("mcr_root"))
-    if params.get("args") is not None:
-        cargs.extend(params.get("args"))
+    cargs.append(params.get("mcr_root", None))
+    if params.get("args", None) is not None:
+        cargs.extend(params.get("args", None))
     return cargs
 
 
@@ -124,9 +98,11 @@ def run_segment_thalamic_nuclei_sh_outputs(
 
 def run_segment_thalamic_nuclei_sh_execute(
     params: RunSegmentThalamicNucleiShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentThalamicNucleiShOutputs:
     """
+    run_SegmentThalamicNuclei.sh
+    
     Script for segmenting thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -135,10 +111,12 @@ def run_segment_thalamic_nuclei_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentThalamicNucleiShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_THALAMIC_NUCLEI_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_thalamic_nuclei_sh_cargs(params, execution)
     ret = run_segment_thalamic_nuclei_sh_outputs(params, execution)
@@ -152,6 +130,8 @@ def run_segment_thalamic_nuclei_sh(
     runner: Runner | None = None,
 ) -> RunSegmentThalamicNucleiShOutputs:
     """
+    run_SegmentThalamicNuclei.sh
+    
     Script for segmenting thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -166,19 +146,17 @@ def run_segment_thalamic_nuclei_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentThalamicNucleiShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_THALAMIC_NUCLEI_SH_METADATA)
     params = run_segment_thalamic_nuclei_sh_params(
         mcr_root=mcr_root,
         args=args,
     )
-    return run_segment_thalamic_nuclei_sh_execute(params, execution)
+    return run_segment_thalamic_nuclei_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_THALAMIC_NUCLEI_SH_METADATA",
     "RunSegmentThalamicNucleiShOutputs",
-    "RunSegmentThalamicNucleiShParameters",
     "run_segment_thalamic_nuclei_sh",
+    "run_segment_thalamic_nuclei_sh_execute",
     "run_segment_thalamic_nuclei_sh_params",
 ]