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

niwrap_freesurfer/freesurfer/mri_ca_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CA_LABEL_METADATA = Metadata(
-    id="035eecaadad51f1937fb29e024f977f0c081a952.boutiques",
+    id="c1394ffdf41a9c43fe2d194cfb7472bc5e4fc8a8.boutiques",
     name="mri_ca_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -19,6 +19,54 @@ MriCaLabelParameters = typing.TypedDict('MriCaLabelParameters', {
     "transform_file": InputPathType,
     "gca_file": InputPathType,
     "output_volume": str,
+    "cross_sequence": bool,
+    "no_gibbs": bool,
+    "wm_segmentation": typing.NotRequired[str | None],
+    "conform": bool,
+    "topo_dist_thresh": typing.NotRequired[float | None],
+    "topo_volume_thresh1": typing.NotRequired[float | None],
+    "topo_volume_thresh2": typing.NotRequired[float | None],
+    "norm_pd": bool,
+    "thin_temporal_lobe": typing.NotRequired[str | None],
+    "debug_voxel": typing.NotRequired[list[float] | None],
+    "debug_node": typing.NotRequired[list[float] | None],
+    "debug_label": typing.NotRequired[float | None],
+    "tr": typing.NotRequired[float | None],
+    "te": typing.NotRequired[float | None],
+    "alpha": typing.NotRequired[float | None],
+    "example": typing.NotRequired[list[InputPathType] | None],
+    "pthresh": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[float | None],
+    "write_probs": typing.NotRequired[str | None],
+    "novar": bool,
+    "regularize": typing.NotRequired[float | None],
+    "nohippo": bool,
+    "fixed_white_matter": typing.NotRequired[str | None],
+    "mri": typing.NotRequired[InputPathType | None],
+    "histogram_equalization": typing.NotRequired[InputPathType | None],
+    "renorm": typing.NotRequired[InputPathType | None],
+    "flash": bool,
+    "flash_params": typing.NotRequired[InputPathType | None],
+    "renormalize": typing.NotRequired[str | None],
+    "set_input_volume": typing.NotRequired[InputPathType | None],
+    "histogram_normalize": bool,
+    "mean_filter": typing.NotRequired[float | None],
+    "write_snapshots": typing.NotRequired[str | None],
+    "mask_final_labeling": typing.NotRequired[InputPathType | None],
+    "expand": typing.NotRequired[float | None],
+    "max_iterations": typing.NotRequired[float | None],
+    "filter_labeled_volume": typing.NotRequired[str | None],
+    "longitudinal_processing": typing.NotRequired[str | None],
+    "relabel_unlikely": typing.NotRequired[str | None],
+    "disables_wmsa": bool,
+    "fix_ventricle": typing.NotRequired[str | None],
+    "insert_wm_bet_putctx": typing.NotRequired[str | None],
+    "sa_insert_wm_bet_putctx": typing.NotRequired[str | None],
+    "insert_from_seg": typing.NotRequired[str | None],
+    "sa_insert_from_seg": typing.NotRequired[str | None],
+    "cblum_from_seg": typing.NotRequired[str | None],
+    "sa_cblum_from_seg": typing.NotRequired[str | None],
+    "threads": typing.NotRequired[int | None],
 })
 
 
@@ -69,6 +117,54 @@ def mri_ca_label_params(
     transform_file: InputPathType,
     gca_file: InputPathType,
     output_volume: str,
+    cross_sequence: bool = False,
+    no_gibbs: bool = False,
+    wm_segmentation: str | None = None,
+    conform: bool = False,
+    topo_dist_thresh: float | None = None,
+    topo_volume_thresh1: float | None = None,
+    topo_volume_thresh2: float | None = None,
+    norm_pd: bool = False,
+    thin_temporal_lobe: str | None = None,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    debug_label: float | None = None,
+    tr: float | None = None,
+    te: float | None = None,
+    alpha: float | None = None,
+    example: list[InputPathType] | None = None,
+    pthresh: float | None = None,
+    niter: float | None = None,
+    write_probs: str | None = None,
+    novar: bool = False,
+    regularize: float | None = None,
+    nohippo: bool = False,
+    fixed_white_matter: str | None = None,
+    mri: InputPathType | None = None,
+    histogram_equalization: InputPathType | None = None,
+    renorm: InputPathType | None = None,
+    flash: bool = False,
+    flash_params: InputPathType | None = None,
+    renormalize: str | None = None,
+    set_input_volume: InputPathType | None = None,
+    histogram_normalize: bool = False,
+    mean_filter: float | None = None,
+    write_snapshots: str | None = None,
+    mask_final_labeling: InputPathType | None = None,
+    expand: float | None = None,
+    max_iterations: float | None = None,
+    filter_labeled_volume: str | None = None,
+    longitudinal_processing: str | None = None,
+    relabel_unlikely: str | None = None,
+    disables_wmsa: bool = False,
+    fix_ventricle: str | None = None,
+    insert_wm_bet_putctx: str | None = None,
+    sa_insert_wm_bet_putctx: str | None = None,
+    insert_from_seg: str | None = None,
+    sa_insert_from_seg: str | None = None,
+    cblum_from_seg: str | None = None,
+    sa_cblum_from_seg: str | None = None,
+    threads: int | None = None,
 ) -> MriCaLabelParameters:
     """
     Build parameters.
@@ -78,6 +174,61 @@ def mri_ca_label_params(
         transform_file: Transform file for the registration.
         gca_file: GCA file for the atlas.
         output_volume: Output labeled volume.
+        cross_sequence: Label a volume acquired with sequence different than\
+            atlas.
+        no_gibbs: Disable gibbs priors.
+        wm_segmentation: Use wm segmentation.
+        conform: Interpolate volume to be isotropic 1mm^3.
+        topo_dist_thresh: Ventricle segments distance threshold.
+        topo_volume_thresh1: First ventricle segments volume threshold.
+        topo_volume_thresh2: Second ventricle segments volume threshold.
+        norm_pd: Normalize PD image to GCA means.
+        thin_temporal_lobe: Use file to label thin temporal lobe.
+        debug_voxel: Debug voxel coordinates.
+        debug_node: Debug node coordinates.
+        debug_label: Debug label.
+        tr: Set TR in msec.
+        te: Set TE in msec.
+        alpha: Set alpha in radians.
+        example: Use T1 and segmentation as example.
+        pthresh: P threshold for adaptive renormalization.
+        niter: Number of iterations for max likelihood.
+        write_probs: Write label probabilities to filename.
+        novar: Do not use variance in classification.
+        regularize: Regularize variance to be sigma+nC(noise).
+        nohippo: Do not auto-edit hippocampus.
+        fixed_white_matter: Use fixed white matter segmentation.
+        mri: Write most likely MR volume to file.
+        histogram_equalization: Use histogram equalization from volume.
+        renorm: Renormalize using predicted intensity values.
+        flash: Use FLASH forward model to predict intensity values.
+        flash_params: Use FLASH forward model and tissue params to predict.
+        renormalize: Renormalize class means iter times after initial label\
+            with window of wsize.
+        set_input_volume: Set input volume.
+        histogram_normalize: Use GCA to histogram normalize input image.
+        mean_filter: Mean filter n time to conditional densities.
+        write_snapshots: Write snapshots of gibbs process every n times to\
+            filename.
+        mask_final_labeling: Use mri_vol to mask final labeling.
+        expand: Expand.
+        max_iterations: Set max iterations.
+        filter_labeled_volume: Filter labeled volume with threshold t.
+        longitudinal_processing: Longitudinal processing with registrations.
+        relabel_unlikely: Reclassify unlikely voxels.
+        disables_wmsa: Disables WMSA labels.
+        fix_ventricle: Fix underlabeled ventricle.
+        insert_wm_bet_putctx: Insert WM between putamen and cortex.
+        sa_insert_wm_bet_putctx: Stand-alone operation to insert WM between\
+            putamen and cortex.
+        insert_from_seg: Insert given indices from segmentation volume.
+        sa_insert_from_seg: Stand-alone insert given indices from segmentation\
+            volume.
+        cblum_from_seg: Insert indices into segmentation volume with default\
+            label set.
+        sa_cblum_from_seg: Stand-alone operation to insert indices into\
+            segmentation with default label set.
+        threads: Set the number of open mp threads.
     Returns:
         Parameter dictionary
     """
@@ -87,7 +238,94 @@ def mri_ca_label_params(
         "transform_file": transform_file,
         "gca_file": gca_file,
         "output_volume": output_volume,
+        "cross_sequence": cross_sequence,
+        "no_gibbs": no_gibbs,
+        "conform": conform,
+        "norm_pd": norm_pd,
+        "novar": novar,
+        "nohippo": nohippo,
+        "flash": flash,
+        "histogram_normalize": histogram_normalize,
+        "disables_wmsa": disables_wmsa,
     }
+    if wm_segmentation is not None:
+        params["wm_segmentation"] = wm_segmentation
+    if topo_dist_thresh is not None:
+        params["topo_dist_thresh"] = topo_dist_thresh
+    if topo_volume_thresh1 is not None:
+        params["topo_volume_thresh1"] = topo_volume_thresh1
+    if topo_volume_thresh2 is not None:
+        params["topo_volume_thresh2"] = topo_volume_thresh2
+    if thin_temporal_lobe is not None:
+        params["thin_temporal_lobe"] = thin_temporal_lobe
+    if debug_voxel is not None:
+        params["debug_voxel"] = debug_voxel
+    if debug_node is not None:
+        params["debug_node"] = debug_node
+    if debug_label is not None:
+        params["debug_label"] = debug_label
+    if tr is not None:
+        params["tr"] = tr
+    if te is not None:
+        params["te"] = te
+    if alpha is not None:
+        params["alpha"] = alpha
+    if example is not None:
+        params["example"] = example
+    if pthresh is not None:
+        params["pthresh"] = pthresh
+    if niter is not None:
+        params["niter"] = niter
+    if write_probs is not None:
+        params["write_probs"] = write_probs
+    if regularize is not None:
+        params["regularize"] = regularize
+    if fixed_white_matter is not None:
+        params["fixed_white_matter"] = fixed_white_matter
+    if mri is not None:
+        params["mri"] = mri
+    if histogram_equalization is not None:
+        params["histogram_equalization"] = histogram_equalization
+    if renorm is not None:
+        params["renorm"] = renorm
+    if flash_params is not None:
+        params["flash_params"] = flash_params
+    if renormalize is not None:
+        params["renormalize"] = renormalize
+    if set_input_volume is not None:
+        params["set_input_volume"] = set_input_volume
+    if mean_filter is not None:
+        params["mean_filter"] = mean_filter
+    if write_snapshots is not None:
+        params["write_snapshots"] = write_snapshots
+    if mask_final_labeling is not None:
+        params["mask_final_labeling"] = mask_final_labeling
+    if expand is not None:
+        params["expand"] = expand
+    if max_iterations is not None:
+        params["max_iterations"] = max_iterations
+    if filter_labeled_volume is not None:
+        params["filter_labeled_volume"] = filter_labeled_volume
+    if longitudinal_processing is not None:
+        params["longitudinal_processing"] = longitudinal_processing
+    if relabel_unlikely is not None:
+        params["relabel_unlikely"] = relabel_unlikely
+    if fix_ventricle is not None:
+        params["fix_ventricle"] = fix_ventricle
+    if insert_wm_bet_putctx is not None:
+        params["insert_wm_bet_putctx"] = insert_wm_bet_putctx
+    if sa_insert_wm_bet_putctx is not None:
+        params["sa_insert_wm_bet_putctx"] = sa_insert_wm_bet_putctx
+    if insert_from_seg is not None:
+        params["insert_from_seg"] = insert_from_seg
+    if sa_insert_from_seg is not None:
+        params["sa_insert_from_seg"] = sa_insert_from_seg
+    if cblum_from_seg is not None:
+        params["cblum_from_seg"] = cblum_from_seg
+    if sa_cblum_from_seg is not None:
+        params["sa_cblum_from_seg"] = sa_cblum_from_seg
+    if threads is not None:
+        params["threads"] = threads
     return params
 
 
@@ -110,7 +348,219 @@ def mri_ca_label_cargs(
     cargs.append(execution.input_file(params.get("transform_file")))
     cargs.append(execution.input_file(params.get("gca_file")))
     cargs.append(params.get("output_volume"))
-    cargs.append("[OPTIONS]")
+    if params.get("cross_sequence"):
+        cargs.append("-cross-sequence")
+    if params.get("no_gibbs"):
+        cargs.append("-nogibbs")
+    if params.get("wm_segmentation") is not None:
+        cargs.extend([
+            "-wm",
+            params.get("wm_segmentation")
+        ])
+    if params.get("conform"):
+        cargs.append("-conform")
+    if params.get("topo_dist_thresh") is not None:
+        cargs.extend([
+            "-topo_dist_thresh",
+            str(params.get("topo_dist_thresh"))
+        ])
+    if params.get("topo_volume_thresh1") is not None:
+        cargs.extend([
+            "-topo_volume_thresh1",
+            str(params.get("topo_volume_thresh1"))
+        ])
+    if params.get("topo_volume_thresh2") is not None:
+        cargs.extend([
+            "-topo_volume_thresh2",
+            str(params.get("topo_volume_thresh2"))
+        ])
+    if params.get("norm_pd"):
+        cargs.append("-normpd")
+    if params.get("thin_temporal_lobe") is not None:
+        cargs.extend([
+            "-tl",
+            params.get("thin_temporal_lobe")
+        ])
+    if params.get("debug_voxel") is not None:
+        cargs.extend([
+            "-debug_voxel",
+            *map(str, params.get("debug_voxel"))
+        ])
+    if params.get("debug_node") is not None:
+        cargs.extend([
+            "-debug_node",
+            *map(str, params.get("debug_node"))
+        ])
+    if params.get("debug_label") is not None:
+        cargs.extend([
+            "-debug_label",
+            str(params.get("debug_label"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-tr",
+            str(params.get("tr"))
+        ])
+    if params.get("te") is not None:
+        cargs.extend([
+            "-te",
+            str(params.get("te"))
+        ])
+    if params.get("alpha") is not None:
+        cargs.extend([
+            "-alpha",
+            str(params.get("alpha"))
+        ])
+    if params.get("example") is not None:
+        cargs.extend([
+            "-example",
+            *[execution.input_file(f) for f in params.get("example")]
+        ])
+    if params.get("pthresh") is not None:
+        cargs.extend([
+            "-pthresh",
+            str(params.get("pthresh"))
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter"))
+        ])
+    if params.get("write_probs") is not None:
+        cargs.extend([
+            "-write_probs",
+            params.get("write_probs")
+        ])
+    if params.get("novar"):
+        cargs.append("-novar")
+    if params.get("regularize") is not None:
+        cargs.extend([
+            "-regularize",
+            str(params.get("regularize"))
+        ])
+    if params.get("nohippo"):
+        cargs.append("-nohippo")
+    if params.get("fixed_white_matter") is not None:
+        cargs.extend([
+            "-fwm",
+            params.get("fixed_white_matter")
+        ])
+    if params.get("mri") is not None:
+        cargs.extend([
+            "-mri",
+            execution.input_file(params.get("mri"))
+        ])
+    if params.get("histogram_equalization") is not None:
+        cargs.extend([
+            "-heq",
+            execution.input_file(params.get("histogram_equalization"))
+        ])
+    if params.get("renorm") is not None:
+        cargs.extend([
+            "-renorm",
+            execution.input_file(params.get("renorm"))
+        ])
+    if params.get("flash"):
+        cargs.append("-flash")
+    if params.get("flash_params") is not None:
+        cargs.extend([
+            "-flash_params",
+            execution.input_file(params.get("flash_params"))
+        ])
+    if params.get("renormalize") is not None:
+        cargs.extend([
+            "-renormalize",
+            params.get("renormalize")
+        ])
+    if params.get("set_input_volume") is not None:
+        cargs.extend([
+            "-r",
+            execution.input_file(params.get("set_input_volume"))
+        ])
+    if params.get("histogram_normalize"):
+        cargs.append("-h")
+    if params.get("mean_filter") is not None:
+        cargs.extend([
+            "-a",
+            str(params.get("mean_filter"))
+        ])
+    if params.get("write_snapshots") is not None:
+        cargs.extend([
+            "-w",
+            params.get("write_snapshots")
+        ])
+    if params.get("mask_final_labeling") is not None:
+        cargs.extend([
+            "-m",
+            execution.input_file(params.get("mask_final_labeling"))
+        ])
+    if params.get("expand") is not None:
+        cargs.extend([
+            "-e",
+            str(params.get("expand"))
+        ])
+    if params.get("max_iterations") is not None:
+        cargs.extend([
+            "-n",
+            str(params.get("max_iterations"))
+        ])
+    if params.get("filter_labeled_volume") is not None:
+        cargs.extend([
+            "-f",
+            params.get("filter_labeled_volume")
+        ])
+    if params.get("longitudinal_processing") is not None:
+        cargs.extend([
+            "-L",
+            params.get("longitudinal_processing")
+        ])
+    if params.get("relabel_unlikely") is not None:
+        cargs.extend([
+            "-RELABEL_UNLIKELY",
+            params.get("relabel_unlikely")
+        ])
+    if params.get("disables_wmsa"):
+        cargs.append("-nowmsa")
+    if params.get("fix_ventricle") is not None:
+        cargs.extend([
+            "-vent-fix",
+            params.get("fix_ventricle")
+        ])
+    if params.get("insert_wm_bet_putctx") is not None:
+        cargs.extend([
+            "-insert-wm-bet-putctx",
+            params.get("insert_wm_bet_putctx")
+        ])
+    if params.get("sa_insert_wm_bet_putctx") is not None:
+        cargs.extend([
+            "-sa-insert-wm-bet-putctx",
+            params.get("sa_insert_wm_bet_putctx")
+        ])
+    if params.get("insert_from_seg") is not None:
+        cargs.extend([
+            "-insert-from-seg",
+            params.get("insert_from_seg")
+        ])
+    if params.get("sa_insert_from_seg") is not None:
+        cargs.extend([
+            "-sa-insert-from-seg",
+            params.get("sa_insert_from_seg")
+        ])
+    if params.get("cblum_from_seg") is not None:
+        cargs.extend([
+            "-cblum-from-seg",
+            params.get("cblum_from_seg")
+        ])
+    if params.get("sa_cblum_from_seg") is not None:
+        cargs.extend([
+            "-sa-cblum-from-seg",
+            params.get("sa_cblum_from_seg")
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "-threads",
+            str(params.get("threads"))
+        ])
     return cargs
 
 
@@ -163,6 +613,54 @@ def mri_ca_label(
     transform_file: InputPathType,
     gca_file: InputPathType,
     output_volume: str,
+    cross_sequence: bool = False,
+    no_gibbs: bool = False,
+    wm_segmentation: str | None = None,
+    conform: bool = False,
+    topo_dist_thresh: float | None = None,
+    topo_volume_thresh1: float | None = None,
+    topo_volume_thresh2: float | None = None,
+    norm_pd: bool = False,
+    thin_temporal_lobe: str | None = None,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    debug_label: float | None = None,
+    tr: float | None = None,
+    te: float | None = None,
+    alpha: float | None = None,
+    example: list[InputPathType] | None = None,
+    pthresh: float | None = None,
+    niter: float | None = None,
+    write_probs: str | None = None,
+    novar: bool = False,
+    regularize: float | None = None,
+    nohippo: bool = False,
+    fixed_white_matter: str | None = None,
+    mri: InputPathType | None = None,
+    histogram_equalization: InputPathType | None = None,
+    renorm: InputPathType | None = None,
+    flash: bool = False,
+    flash_params: InputPathType | None = None,
+    renormalize: str | None = None,
+    set_input_volume: InputPathType | None = None,
+    histogram_normalize: bool = False,
+    mean_filter: float | None = None,
+    write_snapshots: str | None = None,
+    mask_final_labeling: InputPathType | None = None,
+    expand: float | None = None,
+    max_iterations: float | None = None,
+    filter_labeled_volume: str | None = None,
+    longitudinal_processing: str | None = None,
+    relabel_unlikely: str | None = None,
+    disables_wmsa: bool = False,
+    fix_ventricle: str | None = None,
+    insert_wm_bet_putctx: str | None = None,
+    sa_insert_wm_bet_putctx: str | None = None,
+    insert_from_seg: str | None = None,
+    sa_insert_from_seg: str | None = None,
+    cblum_from_seg: str | None = None,
+    sa_cblum_from_seg: str | None = None,
+    threads: int | None = None,
     runner: Runner | None = None,
 ) -> MriCaLabelOutputs:
     """
@@ -177,6 +675,61 @@ def mri_ca_label(
         transform_file: Transform file for the registration.
         gca_file: GCA file for the atlas.
         output_volume: Output labeled volume.
+        cross_sequence: Label a volume acquired with sequence different than\
+            atlas.
+        no_gibbs: Disable gibbs priors.
+        wm_segmentation: Use wm segmentation.
+        conform: Interpolate volume to be isotropic 1mm^3.
+        topo_dist_thresh: Ventricle segments distance threshold.
+        topo_volume_thresh1: First ventricle segments volume threshold.
+        topo_volume_thresh2: Second ventricle segments volume threshold.
+        norm_pd: Normalize PD image to GCA means.
+        thin_temporal_lobe: Use file to label thin temporal lobe.
+        debug_voxel: Debug voxel coordinates.
+        debug_node: Debug node coordinates.
+        debug_label: Debug label.
+        tr: Set TR in msec.
+        te: Set TE in msec.
+        alpha: Set alpha in radians.
+        example: Use T1 and segmentation as example.
+        pthresh: P threshold for adaptive renormalization.
+        niter: Number of iterations for max likelihood.
+        write_probs: Write label probabilities to filename.
+        novar: Do not use variance in classification.
+        regularize: Regularize variance to be sigma+nC(noise).
+        nohippo: Do not auto-edit hippocampus.
+        fixed_white_matter: Use fixed white matter segmentation.
+        mri: Write most likely MR volume to file.
+        histogram_equalization: Use histogram equalization from volume.
+        renorm: Renormalize using predicted intensity values.
+        flash: Use FLASH forward model to predict intensity values.
+        flash_params: Use FLASH forward model and tissue params to predict.
+        renormalize: Renormalize class means iter times after initial label\
+            with window of wsize.
+        set_input_volume: Set input volume.
+        histogram_normalize: Use GCA to histogram normalize input image.
+        mean_filter: Mean filter n time to conditional densities.
+        write_snapshots: Write snapshots of gibbs process every n times to\
+            filename.
+        mask_final_labeling: Use mri_vol to mask final labeling.
+        expand: Expand.
+        max_iterations: Set max iterations.
+        filter_labeled_volume: Filter labeled volume with threshold t.
+        longitudinal_processing: Longitudinal processing with registrations.
+        relabel_unlikely: Reclassify unlikely voxels.
+        disables_wmsa: Disables WMSA labels.
+        fix_ventricle: Fix underlabeled ventricle.
+        insert_wm_bet_putctx: Insert WM between putamen and cortex.
+        sa_insert_wm_bet_putctx: Stand-alone operation to insert WM between\
+            putamen and cortex.
+        insert_from_seg: Insert given indices from segmentation volume.
+        sa_insert_from_seg: Stand-alone insert given indices from segmentation\
+            volume.
+        cblum_from_seg: Insert indices into segmentation volume with default\
+            label set.
+        sa_cblum_from_seg: Stand-alone operation to insert indices into\
+            segmentation with default label set.
+        threads: Set the number of open mp threads.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCaLabelOutputs`).
@@ -188,6 +741,54 @@ def mri_ca_label(
         transform_file=transform_file,
         gca_file=gca_file,
         output_volume=output_volume,
+        cross_sequence=cross_sequence,
+        no_gibbs=no_gibbs,
+        wm_segmentation=wm_segmentation,
+        conform=conform,
+        topo_dist_thresh=topo_dist_thresh,
+        topo_volume_thresh1=topo_volume_thresh1,
+        topo_volume_thresh2=topo_volume_thresh2,
+        norm_pd=norm_pd,
+        thin_temporal_lobe=thin_temporal_lobe,
+        debug_voxel=debug_voxel,
+        debug_node=debug_node,
+        debug_label=debug_label,
+        tr=tr,
+        te=te,
+        alpha=alpha,
+        example=example,
+        pthresh=pthresh,
+        niter=niter,
+        write_probs=write_probs,
+        novar=novar,
+        regularize=regularize,
+        nohippo=nohippo,
+        fixed_white_matter=fixed_white_matter,
+        mri=mri,
+        histogram_equalization=histogram_equalization,
+        renorm=renorm,
+        flash=flash,
+        flash_params=flash_params,
+        renormalize=renormalize,
+        set_input_volume=set_input_volume,
+        histogram_normalize=histogram_normalize,
+        mean_filter=mean_filter,
+        write_snapshots=write_snapshots,
+        mask_final_labeling=mask_final_labeling,
+        expand=expand,
+        max_iterations=max_iterations,
+        filter_labeled_volume=filter_labeled_volume,
+        longitudinal_processing=longitudinal_processing,
+        relabel_unlikely=relabel_unlikely,
+        disables_wmsa=disables_wmsa,
+        fix_ventricle=fix_ventricle,
+        insert_wm_bet_putctx=insert_wm_bet_putctx,
+        sa_insert_wm_bet_putctx=sa_insert_wm_bet_putctx,
+        insert_from_seg=insert_from_seg,
+        sa_insert_from_seg=sa_insert_from_seg,
+        cblum_from_seg=cblum_from_seg,
+        sa_cblum_from_seg=sa_cblum_from_seg,
+        threads=threads,
     )
     return mri_ca_label_execute(params, execution)