niwrap-freesurfer 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/trac_all.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAC_ALL_METADATA = Metadata(
-    id="73a5f89795c73c559ddd404cdcdd1e92ea957a5a.boutiques",
+    id="b42a3b054e835eeb20b6882531177ef5ca819af7.boutiques",
     name="trac-all",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,8 +18,36 @@ TracAllParameters = typing.TypedDict('TracAllParameters', {
     "config_file": typing.NotRequired[InputPathType | None],
     "subject_name": typing.NotRequired[str | None],
     "dicom_file": typing.NotRequired[InputPathType | None],
+    "pre_processing": bool,
+    "bedpost": bool,
+    "pathway_reconstruction": bool,
     "assemble_measures": bool,
+    "image_corrections": bool,
+    "no_image_corrections": bool,
+    "image_quality_assessment": bool,
+    "no_image_quality_assessment": bool,
+    "intra_registration": bool,
+    "no_intra_registration": bool,
+    "tensor_fit": bool,
+    "no_tensor_fit": bool,
+    "inter_registration": bool,
+    "no_inter_registration": bool,
+    "pathway_priors": bool,
     "no_pathway_priors": bool,
+    "infant_options": bool,
+    "job_file": typing.NotRequired[InputPathType | None],
+    "log_file": typing.NotRequired[str | None],
+    "no_append_log": bool,
+    "cmd_file": typing.NotRequired[str | None],
+    "no_is_running": bool,
+    "subjects_directory": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "group_id": typing.NotRequired[str | None],
+    "allow_core_dump": bool,
+    "debug_mode": bool,
+    "dont_run": bool,
+    "only_versions": bool,
+    "version_info": bool,
     "help": bool,
 })
 
@@ -72,8 +100,36 @@ def trac_all_params(
     config_file: InputPathType | None = None,
     subject_name: str | None = None,
     dicom_file: InputPathType | None = None,
+    pre_processing: bool = False,
+    bedpost: bool = False,
+    pathway_reconstruction: bool = False,
     assemble_measures: bool = False,
+    image_corrections: bool = False,
+    no_image_corrections: bool = False,
+    image_quality_assessment: bool = False,
+    no_image_quality_assessment: bool = False,
+    intra_registration: bool = False,
+    no_intra_registration: bool = False,
+    tensor_fit: bool = False,
+    no_tensor_fit: bool = False,
+    inter_registration: bool = False,
+    no_inter_registration: bool = False,
+    pathway_priors: bool = False,
     no_pathway_priors: bool = False,
+    infant_options: bool = False,
+    job_file: InputPathType | None = None,
+    log_file: str | None = None,
+    no_append_log: bool = False,
+    cmd_file: str | None = None,
+    no_is_running: bool = False,
+    subjects_directory: str | None = None,
+    umask: str | None = None,
+    group_id: str | None = None,
+    allow_core_dump: bool = False,
+    debug_mode: bool = False,
+    dont_run: bool = False,
+    only_versions: bool = False,
+    version_info: bool = False,
     help_: bool = False,
 ) -> TracAllParameters:
     """
@@ -83,17 +139,70 @@ def trac_all_params(
         config_file: Configuration file to set analysis options (dmrirc file).
         subject_name: Subject name (if not defined in dmrirc).
         dicom_file: Input DWI DICOM (if not defined in dmrirc).
+        pre_processing: Perform pre-processing (step 1, all substeps).
+        bedpost: Perform bedpost (step 2).
+        pathway_reconstruction: Perform pathway reconstruction (step 3).
         assemble_measures: Assemble pathway measures from multiple subjects\
             (step 4).
+        image_corrections: Perform image corrections (step 1.1).
+        no_image_corrections: Skip image corrections (step 1.1).
+        image_quality_assessment: Perform image quality assessment (step 1.2).
+        no_image_quality_assessment: Skip image quality assessment (step 1.2).
+        intra_registration: Perform intra-subject registration (step 1.3).
+        no_intra_registration: Skip intra-subject registration (step 1.3).
+        tensor_fit: Perform tensor fit (step 1.4).
+        no_tensor_fit: Skip tensor fit (step 1.4).
+        inter_registration: Perform inter-subject registration (step 1.5).
+        no_inter_registration: Skip inter-subject registration (step 1.5).
+        pathway_priors: Perform pathway priors (step 1.6).
         no_pathway_priors: Skip pathway priors (step 1.6).
+        infant_options: Use infant brain processing options.
+        job_file: Write a text file with command lines that can be run in\
+            parallel and do not run them.
+        log_file: Unique log file instead of the default scripts/trac-all.log.
+        no_append_log: Overwrite old log files instead of appending.
+        cmd_file: Unique cmd file instead of the default scripts/trac-all.cmd.
+        no_is_running: Do not check whether subjects are currently being\
+            processed.
+        subjects_directory: Specify subjects directory (default environment\
+            SUBJECTS_DIR).
+        umask: Set Unix file permission mask (default 002).
+        group_id: Check that current group is alpha groupid.
+        allow_core_dump: Set coredump limit to unlimited.
+        debug_mode: Generate much more output.
+        dont_run: Do everything but execute each command.
+        only_versions: Print version of each binary and exit.
+        version_info: Print version of this script and exit.
         help_: Print full contents of help.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "trac-all",
+        "pre_processing": pre_processing,
+        "bedpost": bedpost,
+        "pathway_reconstruction": pathway_reconstruction,
         "assemble_measures": assemble_measures,
+        "image_corrections": image_corrections,
+        "no_image_corrections": no_image_corrections,
+        "image_quality_assessment": image_quality_assessment,
+        "no_image_quality_assessment": no_image_quality_assessment,
+        "intra_registration": intra_registration,
+        "no_intra_registration": no_intra_registration,
+        "tensor_fit": tensor_fit,
+        "no_tensor_fit": no_tensor_fit,
+        "inter_registration": inter_registration,
+        "no_inter_registration": no_inter_registration,
+        "pathway_priors": pathway_priors,
         "no_pathway_priors": no_pathway_priors,
+        "infant_options": infant_options,
+        "no_append_log": no_append_log,
+        "no_is_running": no_is_running,
+        "allow_core_dump": allow_core_dump,
+        "debug_mode": debug_mode,
+        "dont_run": dont_run,
+        "only_versions": only_versions,
+        "version_info": version_info,
         "help": help_,
     }
     if config_file is not None:
@@ -102,6 +211,18 @@ def trac_all_params(
         params["subject_name"] = subject_name
     if dicom_file is not None:
         params["dicom_file"] = dicom_file
+    if job_file is not None:
+        params["job_file"] = job_file
+    if log_file is not None:
+        params["log_file"] = log_file
+    if cmd_file is not None:
+        params["cmd_file"] = cmd_file
+    if subjects_directory is not None:
+        params["subjects_directory"] = subjects_directory
+    if umask is not None:
+        params["umask"] = umask
+    if group_id is not None:
+        params["group_id"] = group_id
     return params
 
 
@@ -135,10 +256,84 @@ def trac_all_cargs(
             "-i",
             execution.input_file(params.get("dicom_file"))
         ])
+    if params.get("pre_processing"):
+        cargs.append("-prep")
+    if params.get("bedpost"):
+        cargs.append("-bedp")
+    if params.get("pathway_reconstruction"):
+        cargs.append("-path")
     if params.get("assemble_measures"):
         cargs.append("-stat")
+    if params.get("image_corrections"):
+        cargs.append("-corr")
+    if params.get("no_image_corrections"):
+        cargs.append("-nocorr")
+    if params.get("image_quality_assessment"):
+        cargs.append("-qa")
+    if params.get("no_image_quality_assessment"):
+        cargs.append("-noqa")
+    if params.get("intra_registration"):
+        cargs.append("-intra")
+    if params.get("no_intra_registration"):
+        cargs.append("-nointra")
+    if params.get("tensor_fit"):
+        cargs.append("-tensor")
+    if params.get("no_tensor_fit"):
+        cargs.append("-notensor")
+    if params.get("inter_registration"):
+        cargs.append("-inter")
+    if params.get("no_inter_registration"):
+        cargs.append("-nointer")
+    if params.get("pathway_priors"):
+        cargs.append("-prior")
     if params.get("no_pathway_priors"):
         cargs.append("-noprior")
+    if params.get("infant_options"):
+        cargs.append("-infant")
+    if params.get("job_file") is not None:
+        cargs.extend([
+            "-jobs",
+            execution.input_file(params.get("job_file"))
+        ])
+    if params.get("log_file") is not None:
+        cargs.extend([
+            "-log",
+            params.get("log_file")
+        ])
+    if params.get("no_append_log"):
+        cargs.append("-noappendlog")
+    if params.get("cmd_file") is not None:
+        cargs.extend([
+            "-cmd",
+            params.get("cmd_file")
+        ])
+    if params.get("no_is_running"):
+        cargs.append("-no-isrunning")
+    if params.get("subjects_directory") is not None:
+        cargs.extend([
+            "-sd",
+            params.get("subjects_directory")
+        ])
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    if params.get("group_id") is not None:
+        cargs.extend([
+            "-grp",
+            params.get("group_id")
+        ])
+    if params.get("allow_core_dump"):
+        cargs.append("-allowcoredump")
+    if params.get("debug_mode"):
+        cargs.append("-debug")
+    if params.get("dont_run"):
+        cargs.append("-dontrun")
+    if params.get("only_versions"):
+        cargs.append("-onlyversions")
+    if params.get("version_info"):
+        cargs.append("-version")
     if params.get("help"):
         cargs.append("-help")
     return cargs
@@ -193,8 +388,36 @@ def trac_all(
     config_file: InputPathType | None = None,
     subject_name: str | None = None,
     dicom_file: InputPathType | None = None,
+    pre_processing: bool = False,
+    bedpost: bool = False,
+    pathway_reconstruction: bool = False,
     assemble_measures: bool = False,
+    image_corrections: bool = False,
+    no_image_corrections: bool = False,
+    image_quality_assessment: bool = False,
+    no_image_quality_assessment: bool = False,
+    intra_registration: bool = False,
+    no_intra_registration: bool = False,
+    tensor_fit: bool = False,
+    no_tensor_fit: bool = False,
+    inter_registration: bool = False,
+    no_inter_registration: bool = False,
+    pathway_priors: bool = False,
     no_pathway_priors: bool = False,
+    infant_options: bool = False,
+    job_file: InputPathType | None = None,
+    log_file: str | None = None,
+    no_append_log: bool = False,
+    cmd_file: str | None = None,
+    no_is_running: bool = False,
+    subjects_directory: str | None = None,
+    umask: str | None = None,
+    group_id: str | None = None,
+    allow_core_dump: bool = False,
+    debug_mode: bool = False,
+    dont_run: bool = False,
+    only_versions: bool = False,
+    version_info: bool = False,
     help_: bool = False,
     runner: Runner | None = None,
 ) -> TracAllOutputs:
@@ -209,9 +432,40 @@ def trac_all(
         config_file: Configuration file to set analysis options (dmrirc file).
         subject_name: Subject name (if not defined in dmrirc).
         dicom_file: Input DWI DICOM (if not defined in dmrirc).
+        pre_processing: Perform pre-processing (step 1, all substeps).
+        bedpost: Perform bedpost (step 2).
+        pathway_reconstruction: Perform pathway reconstruction (step 3).
         assemble_measures: Assemble pathway measures from multiple subjects\
             (step 4).
+        image_corrections: Perform image corrections (step 1.1).
+        no_image_corrections: Skip image corrections (step 1.1).
+        image_quality_assessment: Perform image quality assessment (step 1.2).
+        no_image_quality_assessment: Skip image quality assessment (step 1.2).
+        intra_registration: Perform intra-subject registration (step 1.3).
+        no_intra_registration: Skip intra-subject registration (step 1.3).
+        tensor_fit: Perform tensor fit (step 1.4).
+        no_tensor_fit: Skip tensor fit (step 1.4).
+        inter_registration: Perform inter-subject registration (step 1.5).
+        no_inter_registration: Skip inter-subject registration (step 1.5).
+        pathway_priors: Perform pathway priors (step 1.6).
         no_pathway_priors: Skip pathway priors (step 1.6).
+        infant_options: Use infant brain processing options.
+        job_file: Write a text file with command lines that can be run in\
+            parallel and do not run them.
+        log_file: Unique log file instead of the default scripts/trac-all.log.
+        no_append_log: Overwrite old log files instead of appending.
+        cmd_file: Unique cmd file instead of the default scripts/trac-all.cmd.
+        no_is_running: Do not check whether subjects are currently being\
+            processed.
+        subjects_directory: Specify subjects directory (default environment\
+            SUBJECTS_DIR).
+        umask: Set Unix file permission mask (default 002).
+        group_id: Check that current group is alpha groupid.
+        allow_core_dump: Set coredump limit to unlimited.
+        debug_mode: Generate much more output.
+        dont_run: Do everything but execute each command.
+        only_versions: Print version of each binary and exit.
+        version_info: Print version of this script and exit.
         help_: Print full contents of help.
         runner: Command runner.
     Returns:
@@ -223,8 +477,36 @@ def trac_all(
         config_file=config_file,
         subject_name=subject_name,
         dicom_file=dicom_file,
+        pre_processing=pre_processing,
+        bedpost=bedpost,
+        pathway_reconstruction=pathway_reconstruction,
         assemble_measures=assemble_measures,
+        image_corrections=image_corrections,
+        no_image_corrections=no_image_corrections,
+        image_quality_assessment=image_quality_assessment,
+        no_image_quality_assessment=no_image_quality_assessment,
+        intra_registration=intra_registration,
+        no_intra_registration=no_intra_registration,
+        tensor_fit=tensor_fit,
+        no_tensor_fit=no_tensor_fit,
+        inter_registration=inter_registration,
+        no_inter_registration=no_inter_registration,
+        pathway_priors=pathway_priors,
         no_pathway_priors=no_pathway_priors,
+        infant_options=infant_options,
+        job_file=job_file,
+        log_file=log_file,
+        no_append_log=no_append_log,
+        cmd_file=cmd_file,
+        no_is_running=no_is_running,
+        subjects_directory=subjects_directory,
+        umask=umask,
+        group_id=group_id,
+        allow_core_dump=allow_core_dump,
+        debug_mode=debug_mode,
+        dont_run=dont_run,
+        only_versions=only_versions,
+        version_info=version_info,
         help_=help_,
     )
     return trac_all_execute(params, execution)

niwrap_freesurfer/freesurfer/train_gcs_atlas.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAIN_GCS_ATLAS_METADATA = Metadata(
-    id="915555870bf5ee316610cc5c539e20a5e0db415f.boutiques",
+    id="94c89e1dfe3d6f19edd5cc1f4b3eeb93c181a16d.boutiques",
     name="train-gcs-atlas",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,8 @@ TrainGcsAtlasParameters = typing.TypedDict('TrainGcsAtlasParameters', {
     "__STYX_TYPE__": typing.Literal["train-gcs-atlas"],
     "manual_parcellation": typing.NotRequired[str | None],
     "subjlist_file": typing.NotRequired[InputPathType | None],
+    "left_hemi": bool,
+    "right_hemi": bool,
     "hemi_spec": typing.NotRequired[str | None],
     "output_gcs": str,
     "surf_reg": typing.NotRequired[InputPathType | None],
@@ -74,6 +76,8 @@ def train_gcs_atlas_params(
     output_gcs: str,
     manual_parcellation: str | None = None,
     subjlist_file: InputPathType | None = None,
+    left_hemi: bool = False,
+    right_hemi: bool = False,
     hemi_spec: str | None = None,
     surf_reg: InputPathType | None = None,
     color_table: InputPathType | None = None,
@@ -89,6 +93,8 @@ def train_gcs_atlas_params(
         output_gcs: Output GCS file.
         manual_parcellation: Manual parcellation; default is aparc_edited.
         subjlist_file: File containing the list of subjects.
+        left_hemi: Left hemisphere processing.
+        right_hemi: Right hemisphere processing.
         hemi_spec: Specify hemisphere for processing.
         surf_reg: Surface registration file; default is sphere.reg.
         color_table: Color table file.
@@ -101,6 +107,8 @@ def train_gcs_atlas_params(
     """
     params = {
         "__STYXTYPE__": "train-gcs-atlas",
+        "left_hemi": left_hemi,
+        "right_hemi": right_hemi,
         "output_gcs": output_gcs,
         "jackknife_flag": jackknife_flag,
     }
@@ -148,6 +156,10 @@ def train_gcs_atlas_cargs(
             "--f",
             execution.input_file(params.get("subjlist_file"))
         ])
+    if params.get("left_hemi"):
+        cargs.append("--lh")
+    if params.get("right_hemi"):
+        cargs.append("--rh")
     if params.get("hemi_spec") is not None:
         cargs.extend([
             "--hemi",
@@ -236,6 +248,8 @@ def train_gcs_atlas(
     output_gcs: str,
     manual_parcellation: str | None = None,
     subjlist_file: InputPathType | None = None,
+    left_hemi: bool = False,
+    right_hemi: bool = False,
     hemi_spec: str | None = None,
     surf_reg: InputPathType | None = None,
     color_table: InputPathType | None = None,
@@ -257,6 +271,8 @@ def train_gcs_atlas(
         output_gcs: Output GCS file.
         manual_parcellation: Manual parcellation; default is aparc_edited.
         subjlist_file: File containing the list of subjects.
+        left_hemi: Left hemisphere processing.
+        right_hemi: Right hemisphere processing.
         hemi_spec: Specify hemisphere for processing.
         surf_reg: Surface registration file; default is sphere.reg.
         color_table: Color table file.
@@ -273,6 +289,8 @@ def train_gcs_atlas(
     params = train_gcs_atlas_params(
         manual_parcellation=manual_parcellation,
         subjlist_file=subjlist_file,
+        left_hemi=left_hemi,
+        right_hemi=right_hemi,
         hemi_spec=hemi_spec,
         output_gcs=output_gcs,
         surf_reg=surf_reg,

niwrap_freesurfer/freesurfer/update_needed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UPDATE_NEEDED_METADATA = Metadata(
-    id="81ad1ec598b447ced529bab2b15819d597e08ec9.boutiques",
+    id="bbeff96a804ee5f7f839128e9a8f2889e0e27e42.boutiques",
     name="UpdateNeeded",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,7 @@ UpdateNeededParameters = typing.TypedDict('UpdateNeededParameters', {
     "__STYX_TYPE__": typing.Literal["UpdateNeeded"],
     "target_file": InputPathType,
     "source_file": InputPathType,
+    "additional_source_files": typing.NotRequired[list[InputPathType] | None],
 })
 
 
@@ -62,6 +63,7 @@ class UpdateNeededOutputs(typing.NamedTuple):
 def update_needed_params(
     target_file: InputPathType,
     source_file: InputPathType,
+    additional_source_files: list[InputPathType] | None = None,
 ) -> UpdateNeededParameters:
     """
     Build parameters.
@@ -69,6 +71,8 @@ def update_needed_params(
     Args:
         target_file: The target file that needs to be updated.
         source_file: The primary source file for updating the target file.
+        additional_source_files: Additional source files for updating the\
+            target file.
     Returns:
         Parameter dictionary
     """
@@ -77,6 +81,8 @@ def update_needed_params(
         "target_file": target_file,
         "source_file": source_file,
     }
+    if additional_source_files is not None:
+        params["additional_source_files"] = additional_source_files
     return params
 
 
@@ -97,7 +103,8 @@ def update_needed_cargs(
     cargs.append("UpdateNeeded")
     cargs.append(execution.input_file(params.get("target_file")))
     cargs.append(execution.input_file(params.get("source_file")))
-    cargs.append("[ADDITIONAL_SOURCE_FILES...]")
+    if params.get("additional_source_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("additional_source_files")])
     return cargs
 
 
@@ -147,6 +154,7 @@ def update_needed_execute(
 def update_needed(
     target_file: InputPathType,
     source_file: InputPathType,
+    additional_source_files: list[InputPathType] | None = None,
     runner: Runner | None = None,
 ) -> UpdateNeededOutputs:
     """
@@ -159,6 +167,8 @@ def update_needed(
     Args:
         target_file: The target file that needs to be updated.
         source_file: The primary source file for updating the target file.
+        additional_source_files: Additional source files for updating the\
+            target file.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UpdateNeededOutputs`).
@@ -168,6 +178,7 @@ def update_needed(
     params = update_needed_params(
         target_file=target_file,
         source_file=source_file,
+        additional_source_files=additional_source_files,
     )
     return update_needed_execute(params, execution)
 

niwrap_freesurfer/freesurfer/vertexvol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VERTEXVOL_METADATA = Metadata(
-    id="43f2f0ece18dc9707df38e81102c8d727e4682e9.boutiques",
+    id="72720dd9559564a7517285d29ffdf9116e4d731a.boutiques",
     name="vertexvol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,8 +16,10 @@ VERTEXVOL_METADATA = Metadata(
 VertexvolParameters = typing.TypedDict('VertexvolParameters', {
     "__STYX_TYPE__": typing.Literal["vertexvol"],
     "subject": str,
+    "left_hemisphere": bool,
     "right_hemisphere": bool,
     "output_file": typing.NotRequired[str | None],
+    "use_th3": bool,
     "no_th3": bool,
 })
 
@@ -66,8 +68,10 @@ class VertexvolOutputs(typing.NamedTuple):
 
 def vertexvol_params(
     subject: str,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     output_file: str | None = "?h.volume",
+    use_th3: bool = False,
     no_th3: bool = False,
 ) -> VertexvolParameters:
     """
@@ -75,8 +79,10 @@ def vertexvol_params(
     
     Args:
         subject: Subject identifier.
+        left_hemisphere: Select left hemisphere.
         right_hemisphere: Select right hemisphere.
         output_file: Output file name, default is ?h.volume.
+        use_th3: Use TH3 method for computation.
         no_th3: Don't use TH3 method for computation.
     Returns:
         Parameter dictionary
@@ -84,7 +90,9 @@ def vertexvol_params(
     params = {
         "__STYXTYPE__": "vertexvol",
         "subject": subject,
+        "left_hemisphere": left_hemisphere,
         "right_hemisphere": right_hemisphere,
+        "use_th3": use_th3,
         "no_th3": no_th3,
     }
     if output_file is not None:
@@ -111,6 +119,8 @@ def vertexvol_cargs(
         "--s",
         params.get("subject")
     ])
+    if params.get("left_hemisphere"):
+        cargs.append("--lh")
     if params.get("right_hemisphere"):
         cargs.append("--rh")
     if params.get("output_file") is not None:
@@ -118,6 +128,8 @@ def vertexvol_cargs(
             "--o",
             params.get("output_file")
         ])
+    if params.get("use_th3"):
+        cargs.append("--th3")
     if params.get("no_th3"):
         cargs.append("--no-th3")
     return cargs
@@ -169,8 +181,10 @@ def vertexvol_execute(
 
 def vertexvol(
     subject: str,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     output_file: str | None = "?h.volume",
+    use_th3: bool = False,
     no_th3: bool = False,
     runner: Runner | None = None,
 ) -> VertexvolOutputs:
@@ -183,8 +197,10 @@ def vertexvol(
     
     Args:
         subject: Subject identifier.
+        left_hemisphere: Select left hemisphere.
         right_hemisphere: Select right hemisphere.
         output_file: Output file name, default is ?h.volume.
+        use_th3: Use TH3 method for computation.
         no_th3: Don't use TH3 method for computation.
         runner: Command runner.
     Returns:
@@ -194,8 +210,10 @@ def vertexvol(
     execution = runner.start_execution(VERTEXVOL_METADATA)
     params = vertexvol_params(
         subject=subject,
+        left_hemisphere=left_hemisphere,
         right_hemisphere=right_hemisphere,
         output_file=output_file,
+        use_th3=use_th3,
         no_th3=no_th3,
     )
     return vertexvol_execute(params, execution)