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

niwrap_freesurfer/freesurfer/mri_ca_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CA_TRAIN_METADATA = Metadata(
-    id="432e0861913c8c1346f736846e22c0107ee5337f.boutiques",
+    id="b0a0862d8bce51400e3699e4c44a4499c82a6c8a.boutiques",
     name="mri_ca_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -23,6 +23,7 @@ MriCaTrainParameters = typing.TypedDict('MriCaTrainParameters', {
     "node_spacing": typing.NotRequired[str | None],
     "prior_spacing": typing.NotRequired[str | None],
     "input_training": typing.NotRequired[list[str] | None],
+    "symmetrize": bool,
     "makesym": typing.NotRequired[list[str] | None],
     "check_symmetry": typing.NotRequired[list[str] | None],
     "sanity_check": bool,
@@ -79,6 +80,7 @@ def mri_ca_train_params(
     node_spacing: str | None = None,
     prior_spacing: str | None = None,
     input_training: list[str] | None = None,
+    symmetrize: bool = False,
     makesym: list[str] | None = None,
     check_symmetry: list[str] | None = None,
     sanity_check: bool = False,
@@ -102,6 +104,7 @@ def mri_ca_train_params(
         prior_spacing: Spacing of class priors in canonical space.
         input_training: Specifying training data, path relative to each\
             subject's MRI directory. Can specify multiple inputs.
+        symmetrize: Symmetrize the atlas after creation.
         makesym: Symmetrize an already existing atlas. Specify input GCA and\
             symmetrized GCA.
         check_symmetry: Check the symmetry of an already existing atlas.\
@@ -117,6 +120,7 @@ def mri_ca_train_params(
         "subjects": subjects,
         "output_gca": output_gca,
         "segmentation": segmentation,
+        "symmetrize": symmetrize,
         "sanity_check": sanity_check,
     }
     if transform is not None:
@@ -186,6 +190,8 @@ def mri_ca_train_cargs(
             "-input",
             *params.get("input_training")
         ])
+    if params.get("symmetrize"):
+        cargs.append("-sym")
     if params.get("makesym") is not None:
         cargs.extend([
             "-makesym",
@@ -264,6 +270,7 @@ def mri_ca_train(
     node_spacing: str | None = None,
     prior_spacing: str | None = None,
     input_training: list[str] | None = None,
+    symmetrize: bool = False,
     makesym: list[str] | None = None,
     check_symmetry: list[str] | None = None,
     sanity_check: bool = False,
@@ -293,6 +300,7 @@ def mri_ca_train(
         prior_spacing: Spacing of class priors in canonical space.
         input_training: Specifying training data, path relative to each\
             subject's MRI directory. Can specify multiple inputs.
+        symmetrize: Symmetrize the atlas after creation.
         makesym: Symmetrize an already existing atlas. Specify input GCA and\
             symmetrized GCA.
         check_symmetry: Check the symmetry of an already existing atlas.\
@@ -315,6 +323,7 @@ def mri_ca_train(
         node_spacing=node_spacing,
         prior_spacing=prior_spacing,
         input_training=input_training,
+        symmetrize=symmetrize,
         makesym=makesym,
         check_symmetry=check_symmetry,
         sanity_check=sanity_check,

niwrap_freesurfer/freesurfer/mri_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CONVERT_METADATA = Metadata(
-    id="072cf5d2422186514e5e2726e7afe06ff330f744.boutiques",
+    id="2815806c64bc2ae2d1911e8294a65422695fdb8a.boutiques",
     name="mri_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,23 @@ MriConvertParameters = typing.TypedDict('MriConvertParameters', {
     "__STYX_TYPE__": typing.Literal["mri_convert"],
     "inp_volume": InputPathType,
     "out_volume": str,
+    "read_only": bool,
+    "no_write": bool,
+    "in_info": bool,
+    "out_info": bool,
+    "in_stats": bool,
+    "out_stats": bool,
+    "upsample": typing.NotRequired[float | None],
+    "force_ras_good": bool,
+    "apply_transform": typing.NotRequired[InputPathType | None],
+    "apply_inverse_transform": typing.NotRequired[InputPathType | None],
+    "in_type": typing.NotRequired[str | None],
+    "out_type": typing.NotRequired[str | None],
+    "in_orientation": typing.NotRequired[str | None],
+    "out_orientation": typing.NotRequired[str | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "bfile_little_endian": bool,
+    "sphinx": bool,
 })
 
 
@@ -65,6 +82,23 @@ class MriConvertOutputs(typing.NamedTuple):
 def mri_convert_params(
     inp_volume: InputPathType,
     out_volume: str,
+    read_only: bool = False,
+    no_write: bool = False,
+    in_info: bool = False,
+    out_info: bool = False,
+    in_stats: bool = False,
+    out_stats: bool = False,
+    upsample: float | None = None,
+    force_ras_good: bool = False,
+    apply_transform: InputPathType | None = None,
+    apply_inverse_transform: InputPathType | None = None,
+    in_type: str | None = None,
+    out_type: str | None = None,
+    in_orientation: str | None = None,
+    out_orientation: str | None = None,
+    scale_factor: float | None = None,
+    bfile_little_endian: bool = False,
+    sphinx: bool = False,
 ) -> MriConvertParameters:
     """
     Build parameters.
@@ -72,6 +106,24 @@ def mri_convert_params(
     Args:
         inp_volume: The input volume file.
         out_volume: The output volume file.
+        read_only: Open in read-only mode.
+        no_write: Do not write output.
+        in_info: Print input volume information.
+        out_info: Print output volume information.
+        in_stats: Print statistics on input volume.
+        out_stats: Print statistics on output volume.
+        upsample: Reduce voxel size by a factor in all dimensions.
+        force_ras_good: Use default when orientation info absent.
+        apply_transform: Apply transform given by xfm or m3z file.
+        apply_inverse_transform: Apply inverse of transform given by xfm or m3z\
+            file.
+        in_type: Specify input file type.
+        out_type: Specify output file type.
+        in_orientation: Specify input orientation.
+        out_orientation: Specify output orientation.
+        scale_factor: Input intensity scale factor.
+        bfile_little_endian: Write out bshort/bfloat files in little endian.
+        sphinx: Reorient to sphinx position.
     Returns:
         Parameter dictionary
     """
@@ -79,7 +131,32 @@ def mri_convert_params(
         "__STYXTYPE__": "mri_convert",
         "inp_volume": inp_volume,
         "out_volume": out_volume,
+        "read_only": read_only,
+        "no_write": no_write,
+        "in_info": in_info,
+        "out_info": out_info,
+        "in_stats": in_stats,
+        "out_stats": out_stats,
+        "force_ras_good": force_ras_good,
+        "bfile_little_endian": bfile_little_endian,
+        "sphinx": sphinx,
     }
+    if upsample is not None:
+        params["upsample"] = upsample
+    if apply_transform is not None:
+        params["apply_transform"] = apply_transform
+    if apply_inverse_transform is not None:
+        params["apply_inverse_transform"] = apply_inverse_transform
+    if in_type is not None:
+        params["in_type"] = in_type
+    if out_type is not None:
+        params["out_type"] = out_type
+    if in_orientation is not None:
+        params["in_orientation"] = in_orientation
+    if out_orientation is not None:
+        params["out_orientation"] = out_orientation
+    if scale_factor is not None:
+        params["scale_factor"] = scale_factor
     return params
 
 
@@ -100,7 +177,64 @@ def mri_convert_cargs(
     cargs.append("mri_convert")
     cargs.append(execution.input_file(params.get("inp_volume")))
     cargs.append(params.get("out_volume"))
-    cargs.append("[OPTIONS]")
+    if params.get("read_only"):
+        cargs.append("-ro")
+    if params.get("no_write"):
+        cargs.append("-nw")
+    if params.get("in_info"):
+        cargs.append("-ii")
+    if params.get("out_info"):
+        cargs.append("-oi")
+    if params.get("in_stats"):
+        cargs.append("-is")
+    if params.get("out_stats"):
+        cargs.append("-os")
+    if params.get("upsample") is not None:
+        cargs.extend([
+            "--upsample",
+            str(params.get("upsample"))
+        ])
+    if params.get("force_ras_good"):
+        cargs.append("--force_ras_good")
+    if params.get("apply_transform") is not None:
+        cargs.extend([
+            "--apply_transform",
+            execution.input_file(params.get("apply_transform"))
+        ])
+    if params.get("apply_inverse_transform") is not None:
+        cargs.extend([
+            "--apply_inverse_transform",
+            execution.input_file(params.get("apply_inverse_transform"))
+        ])
+    if params.get("in_type") is not None:
+        cargs.extend([
+            "--in_type",
+            params.get("in_type")
+        ])
+    if params.get("out_type") is not None:
+        cargs.extend([
+            "--out_type",
+            params.get("out_type")
+        ])
+    if params.get("in_orientation") is not None:
+        cargs.extend([
+            "--in_orientation",
+            params.get("in_orientation")
+        ])
+    if params.get("out_orientation") is not None:
+        cargs.extend([
+            "--out_orientation",
+            params.get("out_orientation")
+        ])
+    if params.get("scale_factor") is not None:
+        cargs.extend([
+            "--scale",
+            str(params.get("scale_factor"))
+        ])
+    if params.get("bfile_little_endian"):
+        cargs.append("--bfile-little-endian")
+    if params.get("sphinx"):
+        cargs.append("--sphinx")
     return cargs
 
 
@@ -152,6 +286,23 @@ def mri_convert_execute(
 def mri_convert(
     inp_volume: InputPathType,
     out_volume: str,
+    read_only: bool = False,
+    no_write: bool = False,
+    in_info: bool = False,
+    out_info: bool = False,
+    in_stats: bool = False,
+    out_stats: bool = False,
+    upsample: float | None = None,
+    force_ras_good: bool = False,
+    apply_transform: InputPathType | None = None,
+    apply_inverse_transform: InputPathType | None = None,
+    in_type: str | None = None,
+    out_type: str | None = None,
+    in_orientation: str | None = None,
+    out_orientation: str | None = None,
+    scale_factor: float | None = None,
+    bfile_little_endian: bool = False,
+    sphinx: bool = False,
     runner: Runner | None = None,
 ) -> MriConvertOutputs:
     """
@@ -165,6 +316,24 @@ def mri_convert(
     Args:
         inp_volume: The input volume file.
         out_volume: The output volume file.
+        read_only: Open in read-only mode.
+        no_write: Do not write output.
+        in_info: Print input volume information.
+        out_info: Print output volume information.
+        in_stats: Print statistics on input volume.
+        out_stats: Print statistics on output volume.
+        upsample: Reduce voxel size by a factor in all dimensions.
+        force_ras_good: Use default when orientation info absent.
+        apply_transform: Apply transform given by xfm or m3z file.
+        apply_inverse_transform: Apply inverse of transform given by xfm or m3z\
+            file.
+        in_type: Specify input file type.
+        out_type: Specify output file type.
+        in_orientation: Specify input orientation.
+        out_orientation: Specify output orientation.
+        scale_factor: Input intensity scale factor.
+        bfile_little_endian: Write out bshort/bfloat files in little endian.
+        sphinx: Reorient to sphinx position.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriConvertOutputs`).
@@ -174,6 +343,23 @@ def mri_convert(
     params = mri_convert_params(
         inp_volume=inp_volume,
         out_volume=out_volume,
+        read_only=read_only,
+        no_write=no_write,
+        in_info=in_info,
+        out_info=out_info,
+        in_stats=in_stats,
+        out_stats=out_stats,
+        upsample=upsample,
+        force_ras_good=force_ras_good,
+        apply_transform=apply_transform,
+        apply_inverse_transform=apply_inverse_transform,
+        in_type=in_type,
+        out_type=out_type,
+        in_orientation=in_orientation,
+        out_orientation=out_orientation,
+        scale_factor=scale_factor,
+        bfile_little_endian=bfile_little_endian,
+        sphinx=sphinx,
     )
     return mri_convert_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mri_fuse_segmentations.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FUSE_SEGMENTATIONS_METADATA = Metadata(
-    id="b42ea2ffd32b62f852b2f074e21005b3ac5e5519.boutiques",
+    id="67b2cf4ce2e0dc86fa5a749705372f955d1fc276.boutiques",
     name="mri_fuse_segmentations",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -21,6 +21,7 @@ MriFuseSegmentationsParameters = typing.TypedDict('MriFuseSegmentationsParameter
     "transforms": typing.NotRequired[list[InputPathType] | None],
     "sigma": typing.NotRequired[float | None],
     "input_file": InputPathType,
+    "output_file": str,
 })
 
 
@@ -71,6 +72,7 @@ def mri_fuse_segmentations_params(
     nocc_asegs: list[InputPathType],
     norm_volumes: list[InputPathType],
     input_file: InputPathType,
+    output_file: str,
     transforms: list[InputPathType] | None = None,
     sigma: float | None = 3.0,
 ) -> MriFuseSegmentationsParameters:
@@ -83,6 +85,7 @@ def mri_fuse_segmentations_params(
             per TP.
         norm_volumes: Path to norm.mgz files, one per TP.
         input_file: Input norm.mgz file.
+        output_file: Resulting fused segmentation as aseg.fused.mgz file.
         transforms: Transform files from each TP to the input norm.mgz, can be\
             LTA, M3Z or identity.nofile.
         sigma: Cross-time sigma (default 3.0).
@@ -95,6 +98,7 @@ def mri_fuse_segmentations_params(
         "nocc_asegs": nocc_asegs,
         "norm_volumes": norm_volumes,
         "input_file": input_file,
+        "output_file": output_file,
     }
     if transforms is not None:
         params["transforms"] = transforms
@@ -141,7 +145,7 @@ def mri_fuse_segmentations_cargs(
             str(params.get("sigma"))
         ])
     cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append("[OUTPUT]")
+    cargs.append(params.get("output_file"))
     return cargs
 
 
@@ -160,7 +164,7 @@ def mri_fuse_segmentations_outputs(
     """
     ret = MriFuseSegmentationsOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("[OUTPUT]"),
+        output_file=execution.output_file(params.get("output_file")),
     )
     return ret
 
@@ -195,6 +199,7 @@ def mri_fuse_segmentations(
     nocc_asegs: list[InputPathType],
     norm_volumes: list[InputPathType],
     input_file: InputPathType,
+    output_file: str,
     transforms: list[InputPathType] | None = None,
     sigma: float | None = 3.0,
     runner: Runner | None = None,
@@ -213,6 +218,7 @@ def mri_fuse_segmentations(
             per TP.
         norm_volumes: Path to norm.mgz files, one per TP.
         input_file: Input norm.mgz file.
+        output_file: Resulting fused segmentation as aseg.fused.mgz file.
         transforms: Transform files from each TP to the input norm.mgz, can be\
             LTA, M3Z or identity.nofile.
         sigma: Cross-time sigma (default 3.0).
@@ -229,6 +235,7 @@ def mri_fuse_segmentations(
         transforms=transforms,
         sigma=sigma,
         input_file=input_file,
+        output_file=output_file,
     )
     return mri_fuse_segmentations_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mri_gcab_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GCAB_TRAIN_METADATA = Metadata(
-    id="5b3336956c10bad5fe64ad5c8c726b6429d9bf74.boutiques",
+    id="25854951f0e7de8635b58728b8a09edd107a327e.boutiques",
     name="mri_gcab_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,7 @@ MRI_GCAB_TRAIN_METADATA = Metadata(
 
 MriGcabTrainParameters = typing.TypedDict('MriGcabTrainParameters', {
     "__STYX_TYPE__": typing.Literal["mri_gcab_train"],
+    "removed_info": typing.NotRequired[str | None],
 })
 
 
@@ -58,17 +59,23 @@ class MriGcabTrainOutputs(typing.NamedTuple):
 
 
 def mri_gcab_train_params(
+    removed_info: str | None = "mri_gcab_train has been removed from this version of freesurfer.",
 ) -> MriGcabTrainParameters:
     """
     Build parameters.
     
     Args:
+        removed_info: Command has been removed from the current version of\
+            FreeSurfer. For further information, please contact the support mailing\
+            list.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "mri_gcab_train",
     }
+    if removed_info is not None:
+        params["removed_info"] = removed_info
     return params
 
 
@@ -87,6 +94,8 @@ def mri_gcab_train_cargs(
     """
     cargs = []
     cargs.append("mri_gcab_train")
+    if params.get("removed_info") is not None:
+        cargs.append(params.get("removed_info"))
     return cargs
 
 
@@ -135,6 +144,7 @@ def mri_gcab_train_execute(
 
 
 def mri_gcab_train(
+    removed_info: str | None = "mri_gcab_train has been removed from this version of freesurfer.",
     runner: Runner | None = None,
 ) -> MriGcabTrainOutputs:
     """
@@ -146,6 +156,9 @@ def mri_gcab_train(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        removed_info: Command has been removed from the current version of\
+            FreeSurfer. For further information, please contact the support mailing\
+            list.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGcabTrainOutputs`).
@@ -153,6 +166,7 @@ def mri_gcab_train(
     runner = runner or get_global_runner()
     execution = runner.start_execution(MRI_GCAB_TRAIN_METADATA)
     params = mri_gcab_train_params(
+        removed_info=removed_info,
     )
     return mri_gcab_train_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mri_gdfglm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GDFGLM_METADATA = Metadata(
-    id="6bfd0a6b2b32f6fa09eb9767dc1f8e35ce2df1d6.boutiques",
+    id="799723e383e86e6f477fa13e70a258bc7ff7f5f8.boutiques",
     name="mri_gdfglm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,7 @@ MRI_GDFGLM_METADATA = Metadata(
 
 MriGdfglmParameters = typing.TypedDict('MriGdfglmParameters', {
     "__STYX_TYPE__": typing.Literal["mri_gdfglm"],
+    "inputs": typing.NotRequired[str | None],
 })
 
 
@@ -62,17 +63,22 @@ class MriGdfglmOutputs(typing.NamedTuple):
 
 
 def mri_gdfglm_params(
+    inputs: str | None = None,
 ) -> MriGdfglmParameters:
     """
     Build parameters.
     
     Args:
+        inputs: Input parameters are not available because the command has been\
+            removed.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "mri_gdfglm",
     }
+    if inputs is not None:
+        params["inputs"] = inputs
     return params
 
 
@@ -91,6 +97,8 @@ def mri_gdfglm_cargs(
     """
     cargs = []
     cargs.append("mri_gdfglm")
+    if params.get("inputs") is not None:
+        cargs.append(params.get("inputs"))
     return cargs
 
 
@@ -139,6 +147,7 @@ def mri_gdfglm_execute(
 
 
 def mri_gdfglm(
+    inputs: str | None = None,
     runner: Runner | None = None,
 ) -> MriGdfglmOutputs:
     """
@@ -149,6 +158,8 @@ def mri_gdfglm(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        inputs: Input parameters are not available because the command has been\
+            removed.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGdfglmOutputs`).
@@ -156,6 +167,7 @@ def mri_gdfglm(
     runner = runner or get_global_runner()
     execution = runner.start_execution(MRI_GDFGLM_METADATA)
     params = mri_gdfglm_params(
+        inputs=inputs,
     )
     return mri_gdfglm_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mri_gtmpvc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GTMPVC_METADATA = Metadata(
-    id="fd930d51e0a8f5012076ae523ec1cb2238ba47c5.boutiques",
+    id="3c3042699fe4320ac7c6849c5d7c614e5a318805.boutiques",
     name="mri_gtmpvc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -20,6 +20,8 @@ MriGtmpvcParameters = typing.TypedDict('MriGtmpvcParameters', {
     "psf": float,
     "segmentation": InputPathType,
     "registration": typing.NotRequired[InputPathType | None],
+    "regheader": bool,
+    "reg_identity": bool,
     "output_directory": str,
     "mask": typing.NotRequired[InputPathType | None],
     "auto_mask": typing.NotRequired[int | None],
@@ -149,6 +151,8 @@ def mri_gtmpvc_params(
     output_directory: str,
     frame: float | None = None,
     registration: InputPathType | None = None,
+    regheader: bool = False,
+    reg_identity: bool = False,
     mask: InputPathType | None = None,
     auto_mask: int | None = None,
     no_reduce_fov: bool = False,
@@ -214,6 +218,8 @@ def mri_gtmpvc_params(
         output_directory: Output directory.
         frame: Only process 0-based frame F from input volume.
         registration: LTA registration file that maps PET to anatomical.
+        regheader: Assume input and seg share scanner space.
+        reg_identity: Assume that input is in anatomical space.
         mask: Ignore areas outside of the mask (in input vol space).
         auto_mask: Automatically compute mask with FWHM and threshold.
         no_reduce_fov: Do not reduce FoV to encompass mask.
@@ -285,6 +291,8 @@ def mri_gtmpvc_params(
         "input_volume": input_volume,
         "psf": psf,
         "segmentation": segmentation,
+        "regheader": regheader,
+        "reg_identity": reg_identity,
         "output_directory": output_directory,
         "no_reduce_fov": no_reduce_fov,
         "reduce_fov_eqodd": reduce_fov_eqodd,
@@ -406,6 +414,10 @@ def mri_gtmpvc_cargs(
             "--reg",
             execution.input_file(params.get("registration"))
         ])
+    if params.get("regheader"):
+        cargs.append("--regheader")
+    if params.get("reg_identity"):
+        cargs.append("--reg-identity")
     cargs.extend([
         "--o",
         params.get("output_directory")
@@ -647,6 +659,8 @@ def mri_gtmpvc(
     output_directory: str,
     frame: float | None = None,
     registration: InputPathType | None = None,
+    regheader: bool = False,
+    reg_identity: bool = False,
     mask: InputPathType | None = None,
     auto_mask: int | None = None,
     no_reduce_fov: bool = False,
@@ -718,6 +732,8 @@ def mri_gtmpvc(
         output_directory: Output directory.
         frame: Only process 0-based frame F from input volume.
         registration: LTA registration file that maps PET to anatomical.
+        regheader: Assume input and seg share scanner space.
+        reg_identity: Assume that input is in anatomical space.
         mask: Ignore areas outside of the mask (in input vol space).
         auto_mask: Automatically compute mask with FWHM and threshold.
         no_reduce_fov: Do not reduce FoV to encompass mask.
@@ -793,6 +809,8 @@ def mri_gtmpvc(
         psf=psf,
         segmentation=segmentation,
         registration=registration,
+        regheader=regheader,
+        reg_identity=reg_identity,
         output_directory=output_directory,
         mask=mask,
         auto_mask=auto_mask,

niwrap_freesurfer/freesurfer/mri_hausdorff_dist.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_HAUSDORFF_DIST_METADATA = Metadata(
-    id="44ae0e98e23c4f3e6ba34eebfe000f22002a6a97.boutiques",
+    id="fcb951f6d5703b00765f951fbd55babee3db2ce4.boutiques",
     name="mri_hausdorff_dist",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -131,7 +131,6 @@ def mri_hausdorff_dist_cargs(
     cargs.append(execution.input_file(params.get("vol1")))
     cargs.append(execution.input_file(params.get("vol2")))
     cargs.append(params.get("output_text_file"))
-    cargs.append("[BINARIZE_FLAG]")
     if params.get("threshold") is not None:
         cargs.extend([
             "-b",