niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/segment_subject_t1_t2_auto_estimate_alveus_ml.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
-    id="66b662691063051c8ba61d222df474fa8c958ee2.boutiques",
+    id="b8d0dbdff76a0b38a78846ad65a3d550ba1098a4.boutiques",
     name="segmentSubjectT1T2_autoEstimateAlveusML",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
 
 
 SegmentSubjectT1T2AutoEstimateAlveusMlParameters = typing.TypedDict('SegmentSubjectT1T2AutoEstimateAlveusMlParameters', {
-    "__STYXTYPE__": typing.Literal["segmentSubjectT1T2_autoEstimateAlveusML"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentSubjectT1T2_autoEstimateAlveusML"]],
+    "input_t1": InputPathType,
+    "input_t2": InputPathType,
+    "output_directory": str,
+    "other_options": typing.NotRequired[str | None],
+})
+SegmentSubjectT1T2AutoEstimateAlveusMlParametersTagged = typing.TypedDict('SegmentSubjectT1T2AutoEstimateAlveusMlParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentSubjectT1T2_autoEstimateAlveusML"],
     "input_t1": InputPathType,
     "input_t2": InputPathType,
     "output_directory": str,
     "other_options": 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 {
-        "segmentSubjectT1T2_autoEstimateAlveusML": segment_subject_t1_t2_auto_estimate_alveus_ml_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 {
-        "segmentSubjectT1T2_autoEstimateAlveusML": segment_subject_t1_t2_auto_estimate_alveus_ml_outputs,
-    }.get(t)
 
 
 class SegmentSubjectT1T2AutoEstimateAlveusMlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_t1_t2_auto_estimate_alveus_ml(...)`.
+    Output object returned when calling `SegmentSubjectT1T2AutoEstimateAlveusMlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml_params(
     input_t2: InputPathType,
     output_directory: str,
     other_options: str | None = None,
-) -> SegmentSubjectT1T2AutoEstimateAlveusMlParameters:
+) -> SegmentSubjectT1T2AutoEstimateAlveusMlParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentSubjectT1T2_autoEstimateAlveusML",
+        "@type": "freesurfer/segmentSubjectT1T2_autoEstimateAlveusML",
         "input_t1": input_t1,
         "input_t2": input_t2,
         "output_directory": output_directory,
@@ -107,11 +82,11 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml_cargs(
     """
     cargs = []
     cargs.append("segmentSubjectT1T2_autoEstimateAlveusML")
-    cargs.append(execution.input_file(params.get("input_t1")))
-    cargs.append(execution.input_file(params.get("input_t2")))
-    cargs.append(params.get("output_directory"))
-    if params.get("other_options") is not None:
-        cargs.append(params.get("other_options"))
+    cargs.append(execution.input_file(params.get("input_t1", None)))
+    cargs.append(execution.input_file(params.get("input_t2", None)))
+    cargs.append(params.get("output_directory", None))
+    if params.get("other_options", None) is not None:
+        cargs.append(params.get("other_options", None))
     return cargs
 
 
@@ -130,16 +105,18 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml_outputs(
     """
     ret = SegmentSubjectT1T2AutoEstimateAlveusMlOutputs(
         root=execution.output_file("."),
-        segmentation_result=execution.output_file(params.get("output_directory") + "/segmentation.nii.gz"),
+        segmentation_result=execution.output_file(params.get("output_directory", None) + "/segmentation.nii.gz"),
     )
     return ret
 
 
 def segment_subject_t1_t2_auto_estimate_alveus_ml_execute(
     params: SegmentSubjectT1T2AutoEstimateAlveusMlParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectT1T2AutoEstimateAlveusMlOutputs:
     """
+    segmentSubjectT1T2_autoEstimateAlveusML
+    
     Tool for automatic estimation of the alveus in MR images using T1 and T2
     contrast.
     
@@ -149,10 +126,12 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT1T2AutoEstimateAlveusMlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = execution.params(params)
     cargs = segment_subject_t1_t2_auto_estimate_alveus_ml_cargs(params, execution)
     ret = segment_subject_t1_t2_auto_estimate_alveus_ml_outputs(params, execution)
@@ -168,6 +147,8 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml(
     runner: Runner | None = None,
 ) -> SegmentSubjectT1T2AutoEstimateAlveusMlOutputs:
     """
+    segmentSubjectT1T2_autoEstimateAlveusML
+    
     Tool for automatic estimation of the alveus in MR images using T1 and T2
     contrast.
     
@@ -184,21 +165,19 @@ def segment_subject_t1_t2_auto_estimate_alveus_ml(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT1T2AutoEstimateAlveusMlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = segment_subject_t1_t2_auto_estimate_alveus_ml_params(
         input_t1=input_t1,
         input_t2=input_t2,
         output_directory=output_directory,
         other_options=other_options,
     )
-    return segment_subject_t1_t2_auto_estimate_alveus_ml_execute(params, execution)
+    return segment_subject_t1_t2_auto_estimate_alveus_ml_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_T1_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA",
     "SegmentSubjectT1T2AutoEstimateAlveusMlOutputs",
-    "SegmentSubjectT1T2AutoEstimateAlveusMlParameters",
     "segment_subject_t1_t2_auto_estimate_alveus_ml",
+    "segment_subject_t1_t2_auto_estimate_alveus_ml_execute",
     "segment_subject_t1_t2_auto_estimate_alveus_ml_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject_t2_auto_estimate_alveus_ml.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
-    id="e6b692a7de46610579fa5e10ad01fb96c5b2f745.boutiques",
+    id="9f5cb14cd3ff5a2e14ff4fca40b5b97c1ac6c3c0.boutiques",
     name="segmentSubjectT2_autoEstimateAlveusML",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
 
 
 SegmentSubjectT2AutoEstimateAlveusMlParameters = typing.TypedDict('SegmentSubjectT2AutoEstimateAlveusMlParameters', {
-    "__STYXTYPE__": typing.Literal["segmentSubjectT2_autoEstimateAlveusML"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentSubjectT2_autoEstimateAlveusML"]],
+    "missing_library": str,
+})
+SegmentSubjectT2AutoEstimateAlveusMlParametersTagged = typing.TypedDict('SegmentSubjectT2AutoEstimateAlveusMlParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentSubjectT2_autoEstimateAlveusML"],
     "missing_library": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segmentSubjectT2_autoEstimateAlveusML": segment_subject_t2_auto_estimate_alveus_ml_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 SegmentSubjectT2AutoEstimateAlveusMlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_t2_auto_estimate_alveus_ml(...)`.
+    Output object returned when calling `SegmentSubjectT2AutoEstimateAlveusMlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class SegmentSubjectT2AutoEstimateAlveusMlOutputs(typing.NamedTuple):
 
 def segment_subject_t2_auto_estimate_alveus_ml_params(
     missing_library: str = "libmwlaunchermain.so: cannot open shared object file",
-) -> SegmentSubjectT2AutoEstimateAlveusMlParameters:
+) -> SegmentSubjectT2AutoEstimateAlveusMlParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def segment_subject_t2_auto_estimate_alveus_ml_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentSubjectT2_autoEstimateAlveusML",
+        "@type": "freesurfer/segmentSubjectT2_autoEstimateAlveusML",
         "missing_library": missing_library,
     }
     return params
@@ -92,7 +65,7 @@ def segment_subject_t2_auto_estimate_alveus_ml_cargs(
     """
     cargs = []
     cargs.append("segmentSubjectT2_autoEstimateAlveusML")
-    cargs.append(params.get("missing_library"))
+    cargs.append(params.get("missing_library", "libmwlaunchermain.so: cannot open shared object file"))
     return cargs
 
 
@@ -117,10 +90,13 @@ def segment_subject_t2_auto_estimate_alveus_ml_outputs(
 
 def segment_subject_t2_auto_estimate_alveus_ml_execute(
     params: SegmentSubjectT2AutoEstimateAlveusMlParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectT2AutoEstimateAlveusMlOutputs:
     """
-    A Freesurfer tool to segment T2 subjects with automatic alveus ML estimation.
+    segmentSubjectT2_autoEstimateAlveusML
+    
+    A Freesurfer tool to segment T2 subjects with automatic alveus ML
+    estimation.
     
     Author: FreeSurfer Developers
     
@@ -128,10 +104,12 @@ def segment_subject_t2_auto_estimate_alveus_ml_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT2AutoEstimateAlveusMlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = execution.params(params)
     cargs = segment_subject_t2_auto_estimate_alveus_ml_cargs(params, execution)
     ret = segment_subject_t2_auto_estimate_alveus_ml_outputs(params, execution)
@@ -144,7 +122,10 @@ def segment_subject_t2_auto_estimate_alveus_ml(
     runner: Runner | None = None,
 ) -> SegmentSubjectT2AutoEstimateAlveusMlOutputs:
     """
-    A Freesurfer tool to segment T2 subjects with automatic alveus ML estimation.
+    segmentSubjectT2_autoEstimateAlveusML
+    
+    A Freesurfer tool to segment T2 subjects with automatic alveus ML
+    estimation.
     
     Author: FreeSurfer Developers
     
@@ -157,18 +138,16 @@ def segment_subject_t2_auto_estimate_alveus_ml(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT2AutoEstimateAlveusMlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = segment_subject_t2_auto_estimate_alveus_ml_params(
         missing_library=missing_library,
     )
-    return segment_subject_t2_auto_estimate_alveus_ml_execute(params, execution)
+    return segment_subject_t2_auto_estimate_alveus_ml_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA",
     "SegmentSubjectT2AutoEstimateAlveusMlOutputs",
-    "SegmentSubjectT2AutoEstimateAlveusMlParameters",
     "segment_subject_t2_auto_estimate_alveus_ml",
+    "segment_subject_t2_auto_estimate_alveus_ml_execute",
     "segment_subject_t2_auto_estimate_alveus_ml_params",
 ]

niwrap_freesurfer/freesurfer/segment_subregions.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBREGIONS_METADATA = Metadata(
-    id="a4fdc2917097b87550ba4c5491a1e24ef6f5d80e.boutiques",
+    id="a23e365a3bdaf28e2566ccd0387371b490a84bc2.boutiques",
     name="segment_subregions",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ SEGMENT_SUBREGIONS_METADATA = Metadata(
 
 
 SegmentSubregionsParameters = typing.TypedDict('SegmentSubregionsParameters', {
-    "__STYXTYPE__": typing.Literal["segment_subregions"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subregions"]],
+    "structure": str,
+    "cross": typing.NotRequired[str | None],
+    "long_base": typing.NotRequired[str | None],
+    "sd": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "temp_dir": typing.NotRequired[str | None],
+    "out_dir": typing.NotRequired[str | None],
+    "debug": bool,
+    "threads": typing.NotRequired[float | None],
+})
+SegmentSubregionsParametersTagged = typing.TypedDict('SegmentSubregionsParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subregions"],
     "structure": str,
     "cross": typing.NotRequired[str | None],
     "long_base": typing.NotRequired[str | None],
@@ -25,42 +37,11 @@ SegmentSubregionsParameters = typing.TypedDict('SegmentSubregionsParameters', {
     "debug": bool,
     "threads": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segment_subregions": segment_subregions_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 SegmentSubregionsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subregions(...)`.
+    Output object returned when calling `SegmentSubregionsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def segment_subregions_params(
     out_dir: str | None = None,
     debug: bool = False,
     threads: float | None = None,
-) -> SegmentSubregionsParameters:
+) -> SegmentSubregionsParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +80,7 @@ def segment_subregions_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subregions",
+        "@type": "freesurfer/segment_subregions",
         "structure": structure,
         "debug": debug,
     }
@@ -135,43 +116,43 @@ def segment_subregions_cargs(
     """
     cargs = []
     cargs.append("segment_subregions")
-    cargs.append(params.get("structure"))
-    if params.get("cross") is not None:
+    cargs.append(params.get("structure", None))
+    if params.get("cross", None) is not None:
         cargs.extend([
             "--cross",
-            params.get("cross")
+            params.get("cross", None)
         ])
-    if params.get("long_base") is not None:
+    if params.get("long_base", None) is not None:
         cargs.extend([
             "--long-base",
-            params.get("long_base")
+            params.get("long_base", None)
         ])
-    if params.get("sd") is not None:
+    if params.get("sd", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("sd")
+            params.get("sd", None)
         ])
-    if params.get("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "--suffix",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("temp_dir") is not None:
+    if params.get("temp_dir", None) is not None:
         cargs.extend([
             "--temp-dir",
-            params.get("temp_dir")
+            params.get("temp_dir", None)
         ])
-    if params.get("out_dir") is not None:
+    if params.get("out_dir", None) is not None:
         cargs.extend([
             "--out-dir",
-            params.get("out_dir")
+            params.get("out_dir", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
     return cargs
 
@@ -197,9 +178,11 @@ def segment_subregions_outputs(
 
 def segment_subregions_execute(
     params: SegmentSubregionsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubregionsOutputs:
     """
+    segment_subregions
+    
     Cross-sectional and longitudinal segmentation for brain structures like
     thalamus, brainstem, and hippo-amygdala.
     
@@ -209,10 +192,12 @@ def segment_subregions_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubregionsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBREGIONS_METADATA)
     params = execution.params(params)
     cargs = segment_subregions_cargs(params, execution)
     ret = segment_subregions_outputs(params, execution)
@@ -233,6 +218,8 @@ def segment_subregions(
     runner: Runner | None = None,
 ) -> SegmentSubregionsOutputs:
     """
+    segment_subregions
+    
     Cross-sectional and longitudinal segmentation for brain structures like
     thalamus, brainstem, and hippo-amygdala.
     
@@ -259,8 +246,6 @@ def segment_subregions(
     Returns:
         NamedTuple of outputs (described in `SegmentSubregionsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBREGIONS_METADATA)
     params = segment_subregions_params(
         structure=structure,
         cross=cross,
@@ -272,13 +257,13 @@ def segment_subregions(
         debug=debug,
         threads=threads,
     )
-    return segment_subregions_execute(params, execution)
+    return segment_subregions_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBREGIONS_METADATA",
     "SegmentSubregionsOutputs",
-    "SegmentSubregionsParameters",
     "segment_subregions",
+    "segment_subregions_execute",
     "segment_subregions_params",
 ]

niwrap_freesurfer/freesurfer/segment_thalamic_nuclei.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_THALAMIC_NUCLEI_METADATA = Metadata(
-    id="b83efa0c0cbb57aea3ba929d8c2d6ab17399c339.boutiques",
+    id="c58974ded86d3485652bb5e12314988d875a05f5.boutiques",
     name="SegmentThalamicNuclei",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ SEGMENT_THALAMIC_NUCLEI_METADATA = Metadata(
 
 
 SegmentThalamicNucleiParameters = typing.TypedDict('SegmentThalamicNucleiParameters', {
-    "__STYXTYPE__": typing.Literal["SegmentThalamicNuclei"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/SegmentThalamicNuclei"]],
+    "t1_image": InputPathType,
+    "output_dir": str,
+})
+SegmentThalamicNucleiParametersTagged = typing.TypedDict('SegmentThalamicNucleiParametersTagged', {
+    "@type": typing.Literal["freesurfer/SegmentThalamicNuclei"],
     "t1_image": InputPathType,
     "output_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SegmentThalamicNuclei": segment_thalamic_nuclei_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 {
-        "SegmentThalamicNuclei": segment_thalamic_nuclei_outputs,
-    }.get(t)
 
 
 class SegmentThalamicNucleiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_thalamic_nuclei(...)`.
+    Output object returned when calling `SegmentThalamicNucleiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class SegmentThalamicNucleiOutputs(typing.NamedTuple):
 def segment_thalamic_nuclei_params(
     t1_image: InputPathType,
     output_dir: str,
-) -> SegmentThalamicNucleiParameters:
+) -> SegmentThalamicNucleiParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def segment_thalamic_nuclei_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SegmentThalamicNuclei",
+        "@type": "freesurfer/SegmentThalamicNuclei",
         "t1_image": t1_image,
         "output_dir": output_dir,
     }
@@ -98,8 +71,8 @@ def segment_thalamic_nuclei_cargs(
     """
     cargs = []
     cargs.append("SegmentThalamicNuclei")
-    cargs.append(execution.input_file(params.get("t1_image")))
-    cargs.append(params.get("output_dir"))
+    cargs.append(execution.input_file(params.get("t1_image", None)))
+    cargs.append(params.get("output_dir", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def segment_thalamic_nuclei_outputs(
     """
     ret = SegmentThalamicNucleiOutputs(
         root=execution.output_file("."),
-        seg_output=execution.output_file(params.get("output_dir") + "/thalamic_nuclei_seg.nii.gz"),
+        seg_output=execution.output_file(params.get("output_dir", None) + "/thalamic_nuclei_seg.nii.gz"),
     )
     return ret
 
 
 def segment_thalamic_nuclei_execute(
     params: SegmentThalamicNucleiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentThalamicNucleiOutputs:
     """
+    SegmentThalamicNuclei
+    
     A tool for segmenting thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def segment_thalamic_nuclei_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentThalamicNucleiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_THALAMIC_NUCLEI_METADATA)
     params = execution.params(params)
     cargs = segment_thalamic_nuclei_cargs(params, execution)
     ret = segment_thalamic_nuclei_outputs(params, execution)
@@ -153,6 +130,8 @@ def segment_thalamic_nuclei(
     runner: Runner | None = None,
 ) -> SegmentThalamicNucleiOutputs:
     """
+    SegmentThalamicNuclei
+    
     A tool for segmenting thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def segment_thalamic_nuclei(
     Returns:
         NamedTuple of outputs (described in `SegmentThalamicNucleiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_THALAMIC_NUCLEI_METADATA)
     params = segment_thalamic_nuclei_params(
         t1_image=t1_image,
         output_dir=output_dir,
     )
-    return segment_thalamic_nuclei_execute(params, execution)
+    return segment_thalamic_nuclei_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_THALAMIC_NUCLEI_METADATA",
     "SegmentThalamicNucleiOutputs",
-    "SegmentThalamicNucleiParameters",
     "segment_thalamic_nuclei",
+    "segment_thalamic_nuclei_execute",
     "segment_thalamic_nuclei_params",
 ]