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

niwrap_freesurfer/freesurfer/mri_compute_seg_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_SEG_OVERLAP_METADATA = Metadata(
-    id="28002ed71580b05451b3cd31d91e0b05078efaf6.boutiques",
+    id="cb7bdb7f79028467f821e5384b1d725873398a3c.boutiques",
     name="mri_compute_seg_overlap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRI_COMPUTE_SEG_OVERLAP_METADATA = Metadata(
 
 
 MriComputeSegOverlapParameters = typing.TypedDict('MriComputeSegOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_seg_overlap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_seg_overlap"]],
+    "segvol1": InputPathType,
+    "segvol2": InputPathType,
+    "log_file": typing.NotRequired[str | None],
+    "mean_log_file": typing.NotRequired[str | None],
+    "std_log_file": typing.NotRequired[str | None],
+    "overall_log_flag": bool,
+    "exclude_cortex_flag": bool,
+    "exclude_wm_flag": bool,
+    "all_labels_flag": bool,
+    "dice_params": typing.NotRequired[str | None],
+})
+MriComputeSegOverlapParametersTagged = typing.TypedDict('MriComputeSegOverlapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_seg_overlap"],
     "segvol1": InputPathType,
     "segvol2": InputPathType,
     "log_file": typing.NotRequired[str | None],
@@ -26,42 +39,11 @@ MriComputeSegOverlapParameters = typing.TypedDict('MriComputeSegOverlapParameter
     "all_labels_flag": bool,
     "dice_params": 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 {
-        "mri_compute_seg_overlap": mri_compute_seg_overlap_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 MriComputeSegOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_seg_overlap(...)`.
+    Output object returned when calling `MriComputeSegOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def mri_compute_seg_overlap_params(
     exclude_wm_flag: bool = False,
     all_labels_flag: bool = False,
     dice_params: str | None = None,
-) -> MriComputeSegOverlapParameters:
+) -> MriComputeSegOverlapParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +86,7 @@ def mri_compute_seg_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_seg_overlap",
+        "@type": "freesurfer/mri_compute_seg_overlap",
         "segvol1": segvol1,
         "segvol2": segvol2,
         "overall_log_flag": overall_log_flag,
@@ -138,35 +120,35 @@ def mri_compute_seg_overlap_cargs(
     """
     cargs = []
     cargs.append("mri_compute_seg_overlap")
-    cargs.append(execution.input_file(params.get("segvol1")))
-    cargs.append(execution.input_file(params.get("segvol2")))
-    if params.get("log_file") is not None:
+    cargs.append(execution.input_file(params.get("segvol1", None)))
+    cargs.append(execution.input_file(params.get("segvol2", None)))
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("mean_log_file") is not None:
+    if params.get("mean_log_file", None) is not None:
         cargs.extend([
             "-mlog",
-            params.get("mean_log_file")
+            params.get("mean_log_file", None)
         ])
-    if params.get("std_log_file") is not None:
+    if params.get("std_log_file", None) is not None:
         cargs.extend([
             "-slog",
-            params.get("std_log_file")
+            params.get("std_log_file", None)
         ])
-    if params.get("overall_log_flag"):
+    if params.get("overall_log_flag", False):
         cargs.append("-olog")
-    if params.get("exclude_cortex_flag"):
+    if params.get("exclude_cortex_flag", False):
         cargs.append("-cortex")
-    if params.get("exclude_wm_flag"):
+    if params.get("exclude_wm_flag", False):
         cargs.append("-wm")
-    if params.get("all_labels_flag"):
+    if params.get("all_labels_flag", False):
         cargs.append("-all_labels")
-    if params.get("dice_params") is not None:
+    if params.get("dice_params", None) is not None:
         cargs.extend([
             "-dice",
-            params.get("dice_params")
+            params.get("dice_params", None)
         ])
     return cargs
 
@@ -192,9 +174,11 @@ def mri_compute_seg_overlap_outputs(
 
 def mri_compute_seg_overlap_execute(
     params: MriComputeSegOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeSegOverlapOutputs:
     """
+    mri_compute_seg_overlap
+    
     Compute coefficients of overlap between segmentation volumes.
     
     Author: FreeSurfer Developers
@@ -203,10 +187,12 @@ def mri_compute_seg_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeSegOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_SEG_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = mri_compute_seg_overlap_cargs(params, execution)
     ret = mri_compute_seg_overlap_outputs(params, execution)
@@ -228,6 +214,8 @@ def mri_compute_seg_overlap(
     runner: Runner | None = None,
 ) -> MriComputeSegOverlapOutputs:
     """
+    mri_compute_seg_overlap
+    
     Compute coefficients of overlap between segmentation volumes.
     
     Author: FreeSurfer Developers
@@ -256,8 +244,6 @@ def mri_compute_seg_overlap(
     Returns:
         NamedTuple of outputs (described in `MriComputeSegOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_SEG_OVERLAP_METADATA)
     params = mri_compute_seg_overlap_params(
         segvol1=segvol1,
         segvol2=segvol2,
@@ -270,13 +256,13 @@ def mri_compute_seg_overlap(
         all_labels_flag=all_labels_flag,
         dice_params=dice_params,
     )
-    return mri_compute_seg_overlap_execute(params, execution)
+    return mri_compute_seg_overlap_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_SEG_OVERLAP_METADATA",
     "MriComputeSegOverlapOutputs",
-    "MriComputeSegOverlapParameters",
     "mri_compute_seg_overlap",
+    "mri_compute_seg_overlap_execute",
     "mri_compute_seg_overlap_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_volume_fractions.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_VOLUME_FRACTIONS_METADATA = Metadata(
-    id="c96073b430ac3150fa69b6683b53f6001b13902e.boutiques",
+    id="accbafaf30228c24ceb75d17b4edd13fde8b245c.boutiques",
     name="mri_compute_volume_fractions",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,35 @@ MRI_COMPUTE_VOLUME_FRACTIONS_METADATA = Metadata(
 
 
 MriComputeVolumeFractionsParameters = typing.TypedDict('MriComputeVolumeFractionsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_volume_fractions"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_volume_fractions"]],
+    "output_stem": str,
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "regheader": typing.NotRequired[str | None],
+    "usf": typing.NotRequired[float | None],
+    "resolution": typing.NotRequired[float | None],
+    "resmm": typing.NotRequired[float | None],
+    "segmentation_file": typing.NotRequired[InputPathType | None],
+    "wsurf": typing.NotRequired[str | None],
+    "psurf": typing.NotRequired[str | None],
+    "no_aseg": bool,
+    "stackfile": typing.NotRequired[str | None],
+    "gmfile": typing.NotRequired[str | None],
+    "no_fill_csf": bool,
+    "dilation": typing.NotRequired[float | None],
+    "out_seg": typing.NotRequired[str | None],
+    "ttseg": typing.NotRequired[str | None],
+    "ttseg_ctab": typing.NotRequired[str | None],
+    "mgz_format": bool,
+    "mgh_format": bool,
+    "nii_format": bool,
+    "nii_gz_format": bool,
+    "ttype_head": bool,
+    "vg_thresh": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+})
+MriComputeVolumeFractionsParametersTagged = typing.TypedDict('MriComputeVolumeFractionsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_volume_fractions"],
     "output_stem": str,
     "registration_file": typing.NotRequired[InputPathType | None],
     "regheader": typing.NotRequired[str | None],
@@ -41,43 +69,11 @@ MriComputeVolumeFractionsParameters = typing.TypedDict('MriComputeVolumeFraction
     "debug": bool,
     "checkopts": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_volume_fractions": mri_compute_volume_fractions_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 {
-        "mri_compute_volume_fractions": mri_compute_volume_fractions_outputs,
-    }.get(t)
 
 
 class MriComputeVolumeFractionsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_volume_fractions(...)`.
+    Output object returned when calling `MriComputeVolumeFractionsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -117,7 +113,7 @@ def mri_compute_volume_fractions_params(
     vg_thresh: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
-) -> MriComputeVolumeFractionsParameters:
+) -> MriComputeVolumeFractionsParametersTagged:
     """
     Build parameters.
     
@@ -160,7 +156,7 @@ def mri_compute_volume_fractions_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_volume_fractions",
+        "@type": "freesurfer/mri_compute_volume_fractions",
         "output_stem": output_stem,
         "no_aseg": no_aseg,
         "no_fill_csf": no_fill_csf,
@@ -222,100 +218,100 @@ def mri_compute_volume_fractions_cargs(
     cargs.append("mri_compute_volume_fractions")
     cargs.extend([
         "--o",
-        params.get("output_stem")
+        params.get("output_stem", None)
     ])
-    if params.get("registration_file") is not None:
+    if params.get("registration_file", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("registration_file"))
+            execution.input_file(params.get("registration_file", None))
         ])
-    if params.get("regheader") is not None:
+    if params.get("regheader", None) is not None:
         cargs.extend([
             "--regheader",
-            params.get("regheader")
+            params.get("regheader", None)
         ])
-    if params.get("usf") is not None:
+    if params.get("usf", None) is not None:
         cargs.extend([
             "--usf",
-            str(params.get("usf"))
+            str(params.get("usf", None))
         ])
-    if params.get("resolution") is not None:
+    if params.get("resolution", None) is not None:
         cargs.extend([
             "--r",
-            str(params.get("resolution"))
+            str(params.get("resolution", None))
         ])
-    if params.get("resmm") is not None:
+    if params.get("resmm", None) is not None:
         cargs.extend([
             "--resmm",
-            str(params.get("resmm"))
+            str(params.get("resmm", None))
         ])
-    if params.get("segmentation_file") is not None:
+    if params.get("segmentation_file", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("segmentation_file"))
+            execution.input_file(params.get("segmentation_file", None))
         ])
-    if params.get("wsurf") is not None:
+    if params.get("wsurf", None) is not None:
         cargs.extend([
             "--wsurf",
-            params.get("wsurf")
+            params.get("wsurf", None)
         ])
-    if params.get("psurf") is not None:
+    if params.get("psurf", None) is not None:
         cargs.extend([
             "--psurf",
-            params.get("psurf")
+            params.get("psurf", None)
         ])
-    if params.get("no_aseg"):
+    if params.get("no_aseg", False):
         cargs.append("--no-aseg")
-    if params.get("stackfile") is not None:
+    if params.get("stackfile", None) is not None:
         cargs.extend([
             "--stack",
-            params.get("stackfile")
+            params.get("stackfile", None)
         ])
-    if params.get("gmfile") is not None:
+    if params.get("gmfile", None) is not None:
         cargs.extend([
             "--gm",
-            params.get("gmfile")
+            params.get("gmfile", None)
         ])
-    if params.get("no_fill_csf"):
+    if params.get("no_fill_csf", False):
         cargs.append("--no-fill-csf")
-    if params.get("dilation") is not None:
+    if params.get("dilation", None) is not None:
         cargs.extend([
             "--dil",
-            str(params.get("dilation"))
+            str(params.get("dilation", None))
         ])
-    if params.get("out_seg") is not None:
+    if params.get("out_seg", None) is not None:
         cargs.extend([
             "--out-seg",
-            params.get("out_seg")
+            params.get("out_seg", None)
         ])
-    if params.get("ttseg") is not None:
+    if params.get("ttseg", None) is not None:
         cargs.extend([
             "--ttseg",
-            params.get("ttseg")
+            params.get("ttseg", None)
         ])
-    if params.get("ttseg_ctab") is not None:
+    if params.get("ttseg_ctab", None) is not None:
         cargs.extend([
             "--ttseg-ctab",
-            params.get("ttseg_ctab")
+            params.get("ttseg_ctab", None)
         ])
-    if params.get("mgz_format"):
+    if params.get("mgz_format", False):
         cargs.append("--mgz")
-    if params.get("mgh_format"):
+    if params.get("mgh_format", False):
         cargs.append("--mgh")
-    if params.get("nii_format"):
+    if params.get("nii_format", False):
         cargs.append("--nii")
-    if params.get("nii_gz_format"):
+    if params.get("nii_gz_format", False):
         cargs.append("--nii.gz")
-    if params.get("ttype_head"):
+    if params.get("ttype_head", False):
         cargs.append("--ttype+head")
-    if params.get("vg_thresh") is not None:
+    if params.get("vg_thresh", None) is not None:
         cargs.extend([
             "--vg-thresh",
-            str(params.get("vg_thresh"))
+            str(params.get("vg_thresh", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -335,19 +331,21 @@ def mri_compute_volume_fractions_outputs(
     """
     ret = MriComputeVolumeFractionsOutputs(
         root=execution.output_file("."),
-        output_cortex=execution.output_file(params.get("output_stem") + ".cortex.mgz"),
-        output_subcort_gm=execution.output_file(params.get("output_stem") + ".subcort_gm.mgz"),
-        output_wm=execution.output_file(params.get("output_stem") + ".wm.mgz"),
-        output_csf=execution.output_file(params.get("output_stem") + ".csf.mgz"),
+        output_cortex=execution.output_file(params.get("output_stem", None) + ".cortex.mgz"),
+        output_subcort_gm=execution.output_file(params.get("output_stem", None) + ".subcort_gm.mgz"),
+        output_wm=execution.output_file(params.get("output_stem", None) + ".wm.mgz"),
+        output_csf=execution.output_file(params.get("output_stem", None) + ".csf.mgz"),
     )
     return ret
 
 
 def mri_compute_volume_fractions_execute(
     params: MriComputeVolumeFractionsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeVolumeFractionsOutputs:
     """
+    mri_compute_volume_fractions
+    
     Computes partial volume fractions for cortex, subcortical GM, WM and CSF.
     
     Author: FreeSurfer Developers
@@ -356,10 +354,12 @@ def mri_compute_volume_fractions_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeVolumeFractionsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_VOLUME_FRACTIONS_METADATA)
     params = execution.params(params)
     cargs = mri_compute_volume_fractions_cargs(params, execution)
     ret = mri_compute_volume_fractions_outputs(params, execution)
@@ -396,6 +396,8 @@ def mri_compute_volume_fractions(
     runner: Runner | None = None,
 ) -> MriComputeVolumeFractionsOutputs:
     """
+    mri_compute_volume_fractions
+    
     Computes partial volume fractions for cortex, subcortical GM, WM and CSF.
     
     Author: FreeSurfer Developers
@@ -441,8 +443,6 @@ def mri_compute_volume_fractions(
     Returns:
         NamedTuple of outputs (described in `MriComputeVolumeFractionsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_VOLUME_FRACTIONS_METADATA)
     params = mri_compute_volume_fractions_params(
         output_stem=output_stem,
         registration_file=registration_file,
@@ -470,13 +470,13 @@ def mri_compute_volume_fractions(
         debug=debug,
         checkopts=checkopts,
     )
-    return mri_compute_volume_fractions_execute(params, execution)
+    return mri_compute_volume_fractions_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_VOLUME_FRACTIONS_METADATA",
     "MriComputeVolumeFractionsOutputs",
-    "MriComputeVolumeFractionsParameters",
     "mri_compute_volume_fractions",
+    "mri_compute_volume_fractions_execute",
     "mri_compute_volume_fractions_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_volume_intensities.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_VOLUME_INTENSITIES_METADATA = Metadata(
-    id="e987ec4c7e20112b9b235a6b1cbc9c288afb0c2d.boutiques",
+    id="223a282c55d0dc7fb7079cb3ae30f18a27d0bf1d.boutiques",
     name="mri_compute_volume_intensities",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_COMPUTE_VOLUME_INTENSITIES_METADATA = Metadata(
 
 
 MriComputeVolumeIntensitiesParameters = typing.TypedDict('MriComputeVolumeIntensitiesParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_volume_intensities"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_volume_intensities"]],
+    "input_intensity": InputPathType,
+    "volume_fraction_stem": str,
+    "output_volume": str,
+})
+MriComputeVolumeIntensitiesParametersTagged = typing.TypedDict('MriComputeVolumeIntensitiesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_volume_intensities"],
     "input_intensity": InputPathType,
     "volume_fraction_stem": str,
     "output_volume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_volume_intensities": mri_compute_volume_intensities_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 {
-        "mri_compute_volume_intensities": mri_compute_volume_intensities_outputs,
-    }.get(t)
 
 
 class MriComputeVolumeIntensitiesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_volume_intensities(...)`.
+    Output object returned when calling `MriComputeVolumeIntensitiesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_compute_volume_intensities_params(
     input_intensity: InputPathType,
     volume_fraction_stem: str,
     output_volume: str,
-) -> MriComputeVolumeIntensitiesParameters:
+) -> MriComputeVolumeIntensitiesParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_compute_volume_intensities_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_volume_intensities",
+        "@type": "freesurfer/mri_compute_volume_intensities",
         "input_intensity": input_intensity,
         "volume_fraction_stem": volume_fraction_stem,
         "output_volume": output_volume,
@@ -102,9 +76,9 @@ def mri_compute_volume_intensities_cargs(
     """
     cargs = []
     cargs.append("mri_compute_volume_intensities")
-    cargs.append(execution.input_file(params.get("input_intensity")))
-    cargs.append(params.get("volume_fraction_stem"))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_intensity", None)))
+    cargs.append(params.get("volume_fraction_stem", None))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_compute_volume_intensities_outputs(
     """
     ret = MriComputeVolumeIntensitiesOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("output_volume")),
+        output_volume_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_compute_volume_intensities_execute(
     params: MriComputeVolumeIntensitiesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeVolumeIntensitiesOutputs:
     """
+    mri_compute_volume_intensities
+    
     A tool to compute volume intensities for a given input intensity volume and
     volume fraction stem.
     
@@ -142,10 +118,12 @@ def mri_compute_volume_intensities_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeVolumeIntensitiesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_VOLUME_INTENSITIES_METADATA)
     params = execution.params(params)
     cargs = mri_compute_volume_intensities_cargs(params, execution)
     ret = mri_compute_volume_intensities_outputs(params, execution)
@@ -160,6 +138,8 @@ def mri_compute_volume_intensities(
     runner: Runner | None = None,
 ) -> MriComputeVolumeIntensitiesOutputs:
     """
+    mri_compute_volume_intensities
+    
     A tool to compute volume intensities for a given input intensity volume and
     volume fraction stem.
     
@@ -175,20 +155,18 @@ def mri_compute_volume_intensities(
     Returns:
         NamedTuple of outputs (described in `MriComputeVolumeIntensitiesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_VOLUME_INTENSITIES_METADATA)
     params = mri_compute_volume_intensities_params(
         input_intensity=input_intensity,
         volume_fraction_stem=volume_fraction_stem,
         output_volume=output_volume,
     )
-    return mri_compute_volume_intensities_execute(params, execution)
+    return mri_compute_volume_intensities_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_VOLUME_INTENSITIES_METADATA",
     "MriComputeVolumeIntensitiesOutputs",
-    "MriComputeVolumeIntensitiesParameters",
     "mri_compute_volume_intensities",
+    "mri_compute_volume_intensities_execute",
     "mri_compute_volume_intensities_params",
 ]