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

niwrap_freesurfer/freesurfer/merge_stats_tables.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MERGE_STATS_TABLES_METADATA = Metadata(
-    id="004967733986569ad699b7fcfc4e0e899cb02c90.boutiques",
+    id="35129fec9b70b3cf111ebb349d44b5a25140111b.boutiques",
     name="merge_stats_tables",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,16 +15,18 @@ MERGE_STATS_TABLES_METADATA = Metadata(
 
 MergeStatsTablesParameters = typing.TypedDict('MergeStatsTablesParameters', {
     "__STYX_TYPE__": typing.Literal["merge_stats_tables"],
+    "subjects": typing.NotRequired[list[str] | None],
     "subject": typing.NotRequired[str | None],
+    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "inputs": typing.NotRequired[list[InputPathType] | None],
     "input": typing.NotRequired[InputPathType | None],
     "outputfile": str,
     "meas": str,
-    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "common_segs": bool,
+    "all_segs": bool,
     "intable": typing.NotRequired[InputPathType | None],
     "subdir": typing.NotRequired[str | None],
     "delimiter": typing.NotRequired[str | None],
-    "common_segs": bool,
-    "all_segs": bool,
     "transpose": bool,
     "skip": bool,
     "debug": bool,
@@ -76,14 +78,16 @@ class MergeStatsTablesOutputs(typing.NamedTuple):
 def merge_stats_tables_params(
     outputfile: str,
     meas: str,
+    subjects: list[str] | None = None,
     subject: str | None = None,
-    input_: InputPathType | None = None,
     subjectsfile: InputPathType | None = None,
+    inputs: list[InputPathType] | None = None,
+    input_: InputPathType | None = None,
+    common_segs: bool = False,
+    all_segs: bool = False,
     intable: InputPathType | None = None,
     subdir: str | None = None,
     delimiter: str | None = None,
-    common_segs: bool = False,
-    all_segs: bool = False,
     transpose: bool = False,
     skip: bool = False,
     debug: bool = False,
@@ -94,18 +98,20 @@ def merge_stats_tables_params(
     Args:
         outputfile: The output table file.
         meas: Measure to write in output table.
+        subjects: Specify the subjects names.
         subject: Specify a single subject name.
-        input_: Specify a single input stat file.
         subjectsfile: Name of the file which has the list of subjects (one\
             subject per line).
+        inputs: Specify all the input stat files.
+        input_: Specify a single input stat file.
+        common_segs: Output only the common segmentations of all the statsfiles\
+            given.
+        all_segs: Output all the segmentations of the statsfiles given.
         intable: Use `fname` as input (REQUIRED when passing subject ids).
         subdir: Use `subdir` instead of default "stats/" when passing subject\
             ids.
         delimiter: Delimiter between measures in the table. Options are 'tab',\
             'space', 'comma', and 'semicolon'. Default is 'space'.
-        common_segs: Output only the common segmentations of all the statsfiles\
-            given.
-        all_segs: Output all the segmentations of the statsfiles given.
         transpose: Transpose the table (default is subjects in rows and\
             segmentations in cols).
         skip: If a subject does not have a stats file, skip it instead of\
@@ -124,12 +130,16 @@ def merge_stats_tables_params(
         "skip": skip,
         "debug": debug,
     }
+    if subjects is not None:
+        params["subjects"] = subjects
     if subject is not None:
         params["subject"] = subject
-    if input_ is not None:
-        params["input"] = input_
     if subjectsfile is not None:
         params["subjectsfile"] = subjectsfile
+    if inputs is not None:
+        params["inputs"] = inputs
+    if input_ is not None:
+        params["input"] = input_
     if intable is not None:
         params["intable"] = intable
     if subdir is not None:
@@ -154,11 +164,26 @@ def merge_stats_tables_cargs(
     """
     cargs = []
     cargs.append("merge_stats_tables")
+    if params.get("subjects") is not None:
+        cargs.extend([
+            "--subjects",
+            *params.get("subjects")
+        ])
     if params.get("subject") is not None:
         cargs.extend([
             "-s",
             params.get("subject")
         ])
+    if params.get("subjectsfile") is not None:
+        cargs.extend([
+            "--subjectsfile",
+            execution.input_file(params.get("subjectsfile"))
+        ])
+    if params.get("inputs") is not None:
+        cargs.extend([
+            "--inputs",
+            *[execution.input_file(f) for f in params.get("inputs")]
+        ])
     if params.get("input") is not None:
         cargs.extend([
             "-i",
@@ -172,11 +197,10 @@ def merge_stats_tables_cargs(
         "-m",
         params.get("meas")
     ])
-    if params.get("subjectsfile") is not None:
-        cargs.extend([
-            "--subjectsfile",
-            execution.input_file(params.get("subjectsfile"))
-        ])
+    if params.get("common_segs"):
+        cargs.append("--common-segs")
+    if params.get("all_segs"):
+        cargs.append("--all-segs")
     if params.get("intable") is not None:
         cargs.extend([
             "--intable",
@@ -192,13 +216,6 @@ def merge_stats_tables_cargs(
             "-d",
             params.get("delimiter")
         ])
-    if params.get("common_segs"):
-        cargs.append("--common-segs")
-    if params.get("all_segs"):
-        cargs.append("--all-segs")
-    cargs.append("[SEGIDS_FROM_FILE]")
-    cargs.append("[SEGNO]")
-    cargs.append("[NO_SEGNO_FLAG]")
     if params.get("transpose"):
         cargs.append("--transpose")
     if params.get("skip"):
@@ -256,14 +273,16 @@ def merge_stats_tables_execute(
 def merge_stats_tables(
     outputfile: str,
     meas: str,
+    subjects: list[str] | None = None,
     subject: str | None = None,
-    input_: InputPathType | None = None,
     subjectsfile: InputPathType | None = None,
+    inputs: list[InputPathType] | None = None,
+    input_: InputPathType | None = None,
+    common_segs: bool = False,
+    all_segs: bool = False,
     intable: InputPathType | None = None,
     subdir: str | None = None,
     delimiter: str | None = None,
-    common_segs: bool = False,
-    all_segs: bool = False,
     transpose: bool = False,
     skip: bool = False,
     debug: bool = False,
@@ -280,18 +299,20 @@ def merge_stats_tables(
     Args:
         outputfile: The output table file.
         meas: Measure to write in output table.
+        subjects: Specify the subjects names.
         subject: Specify a single subject name.
-        input_: Specify a single input stat file.
         subjectsfile: Name of the file which has the list of subjects (one\
             subject per line).
+        inputs: Specify all the input stat files.
+        input_: Specify a single input stat file.
+        common_segs: Output only the common segmentations of all the statsfiles\
+            given.
+        all_segs: Output all the segmentations of the statsfiles given.
         intable: Use `fname` as input (REQUIRED when passing subject ids).
         subdir: Use `subdir` instead of default "stats/" when passing subject\
             ids.
         delimiter: Delimiter between measures in the table. Options are 'tab',\
             'space', 'comma', and 'semicolon'. Default is 'space'.
-        common_segs: Output only the common segmentations of all the statsfiles\
-            given.
-        all_segs: Output all the segmentations of the statsfiles given.
         transpose: Transpose the table (default is subjects in rows and\
             segmentations in cols).
         skip: If a subject does not have a stats file, skip it instead of\
@@ -304,16 +325,18 @@ def merge_stats_tables(
     runner = runner or get_global_runner()
     execution = runner.start_execution(MERGE_STATS_TABLES_METADATA)
     params = merge_stats_tables_params(
+        subjects=subjects,
         subject=subject,
+        subjectsfile=subjectsfile,
+        inputs=inputs,
         input_=input_,
         outputfile=outputfile,
         meas=meas,
-        subjectsfile=subjectsfile,
+        common_segs=common_segs,
+        all_segs=all_segs,
         intable=intable,
         subdir=subdir,
         delimiter=delimiter,
-        common_segs=common_segs,
-        all_segs=all_segs,
         transpose=transpose,
         skip=skip,
         debug=debug,

niwrap_freesurfer/freesurfer/mideface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MIDEFACE_METADATA = Metadata(
-    id="78ed8c9b1bc484046f26f89a611375e8c4e503a1.boutiques",
+    id="e4a7d1cf3f8f93ccdd73f64b12dba5ce0fe4110b.boutiques",
     name="mideface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -22,18 +22,29 @@ MidefaceParameters = typing.TypedDict('MidefaceParameters', {
     "exclusion_mask": typing.NotRequired[InputPathType | None],
     "samseg_ndilations": typing.NotRequired[float | None],
     "samseg_json": typing.NotRequired[str | None],
+    "samseg_fast": bool,
+    "no_samseg_fast": bool,
     "init_reg": typing.NotRequired[InputPathType | None],
     "synthseg_ndilations": typing.NotRequired[float | None],
     "fill_const": typing.NotRequired[list[float] | None],
+    "fill_zero": bool,
     "fhi": typing.NotRequired[float | None],
+    "no_ears": bool,
+    "back_of_head": bool,
+    "forehead": bool,
+    "pics": bool,
     "code": typing.NotRequired[str | None],
     "image_convert": typing.NotRequired[str | None],
+    "no_post": bool,
     "threads": typing.NotRequired[float | None],
+    "force": bool,
+    "output_format": typing.NotRequired[str | None],
+    "atlas": typing.NotRequired[str | None],
+    "expert": typing.NotRequired[str | None],
     "display_no": typing.NotRequired[float | None],
     "apply_volume": typing.NotRequired[str | None],
     "check_volume": typing.NotRequired[InputPathType | None],
     "check_output_file": typing.NotRequired[InputPathType | None],
-    "output_format": typing.NotRequired[str | None],
 })
 
 
@@ -89,18 +100,29 @@ def mideface_params(
     exclusion_mask: InputPathType | None = None,
     samseg_ndilations: float | None = None,
     samseg_json: str | None = None,
+    samseg_fast: bool = False,
+    no_samseg_fast: bool = False,
     init_reg: InputPathType | None = None,
     synthseg_ndilations: float | None = None,
     fill_const: list[float] | None = None,
+    fill_zero: bool = False,
     fhi: float | None = None,
+    no_ears: bool = False,
+    back_of_head: bool = False,
+    forehead: bool = False,
+    pics: bool = False,
     code_: str | None = None,
     image_convert: str | None = None,
+    no_post: bool = False,
     threads: float | None = None,
+    force: bool = False,
+    output_format: str | None = None,
+    atlas: str | None = None,
+    expert: str | None = None,
     display_no: float | None = None,
     apply_volume: str | None = None,
     check_volume: InputPathType | None = None,
     check_output_file: InputPathType | None = None,
-    output_format: str | None = None,
 ) -> MidefaceParameters:
     """
     Build parameters.
@@ -113,18 +135,29 @@ def mideface_params(
         exclusion_mask: Mask to exclude certain regions from defacing.
         samseg_ndilations: Number of dilations for Samseg segmentation.
         samseg_json: JSON configuration for Samseg.
+        samseg_fast: Configure Samseg to run quickly.
+        no_samseg_fast: Do not configure Samseg to run quickly.
         init_reg: Initial registration file for Samseg.
         synthseg_ndilations: Number of dilations for Synthseg segmentation.
         fill_const: Constants for filling regions.
+        fill_zero: Fill regions with zero.
         fhi: FHI value for MRIchangeType().
+        no_ears: Do not include ears in the defacing.
+        back_of_head: Include back of head in defacing.
+        forehead: Include forehead in defacing (risks removing brain).
+        pics: Take pictures of the defaced result.
         code_: Embed code name in pictures.
         image_convert: Path to ImageMagick convert binary for pictures.
+        no_post: Do not make a head surface after defacing.
         threads: Number of threads to use.
+        force: Force reprocessing (only applicable if output directory is used).
+        output_format: Output file format.
+        atlas: Directory containing atlas files.
+        expert: Additional expert options.
         display_no: Xvfb display number for taking pictures.
         apply_volume: Apply midface output to a second volume.
         check_volume: Volume to check if defaced.
         check_output_file: Optional output file for check result.
-        output_format: Output file format.
     Returns:
         Parameter dictionary
     """
@@ -132,6 +165,15 @@ def mideface_params(
         "__STYXTYPE__": "mideface",
         "input_volume": input_volume,
         "output_volume": output_volume,
+        "samseg_fast": samseg_fast,
+        "no_samseg_fast": no_samseg_fast,
+        "fill_zero": fill_zero,
+        "no_ears": no_ears,
+        "back_of_head": back_of_head,
+        "forehead": forehead,
+        "pics": pics,
+        "no_post": no_post,
+        "force": force,
     }
     if facemask is not None:
         params["facemask"] = facemask
@@ -157,6 +199,12 @@ def mideface_params(
         params["image_convert"] = image_convert
     if threads is not None:
         params["threads"] = threads
+    if output_format is not None:
+        params["output_format"] = output_format
+    if atlas is not None:
+        params["atlas"] = atlas
+    if expert is not None:
+        params["expert"] = expert
     if display_no is not None:
         params["display_no"] = display_no
     if apply_volume is not None:
@@ -165,8 +213,6 @@ def mideface_params(
         params["check_volume"] = check_volume
     if check_output_file is not None:
         params["check_output_file"] = check_output_file
-    if output_format is not None:
-        params["output_format"] = output_format
     return params
 
 
@@ -218,6 +264,10 @@ def mideface_cargs(
             "--samseg-json",
             params.get("samseg_json")
         ])
+    if params.get("samseg_fast"):
+        cargs.append("--samseg-fast")
+    if params.get("no_samseg_fast"):
+        cargs.append("--no-samseg-fast")
     if params.get("init_reg") is not None:
         cargs.extend([
             "--init-reg",
@@ -233,11 +283,21 @@ def mideface_cargs(
             "--fill-const",
             *map(str, params.get("fill_const"))
         ])
+    if params.get("fill_zero"):
+        cargs.append("--fill-zero")
     if params.get("fhi") is not None:
         cargs.extend([
             "--fhi",
             str(params.get("fhi"))
         ])
+    if params.get("no_ears"):
+        cargs.append("--no-ears")
+    if params.get("back_of_head"):
+        cargs.append("--back-of-head")
+    if params.get("forehead"):
+        cargs.append("--forehead")
+    if params.get("pics"):
+        cargs.append("--pics")
     if params.get("code") is not None:
         cargs.extend([
             "--code",
@@ -248,11 +308,30 @@ def mideface_cargs(
             "--imconvert",
             params.get("image_convert")
         ])
+    if params.get("no_post"):
+        cargs.append("--no-post")
     if params.get("threads") is not None:
         cargs.extend([
             "--threads",
             str(params.get("threads"))
         ])
+    if params.get("force"):
+        cargs.append("--force")
+    if params.get("output_format") is not None:
+        cargs.extend([
+            "--nii --nii.gz --mgz",
+            params.get("output_format")
+        ])
+    if params.get("atlas") is not None:
+        cargs.extend([
+            "--atlas",
+            params.get("atlas")
+        ])
+    if params.get("expert") is not None:
+        cargs.extend([
+            "--expert",
+            params.get("expert")
+        ])
     if params.get("display_no") is not None:
         cargs.extend([
             "--display",
@@ -273,11 +352,6 @@ def mideface_cargs(
             "--check",
             execution.input_file(params.get("check_output_file"))
         ])
-    if params.get("output_format") is not None:
-        cargs.extend([
-            "--nii --nii.gz --mgz",
-            params.get("output_format")
-        ])
     return cargs
 
 
@@ -334,18 +408,29 @@ def mideface(
     exclusion_mask: InputPathType | None = None,
     samseg_ndilations: float | None = None,
     samseg_json: str | None = None,
+    samseg_fast: bool = False,
+    no_samseg_fast: bool = False,
     init_reg: InputPathType | None = None,
     synthseg_ndilations: float | None = None,
     fill_const: list[float] | None = None,
+    fill_zero: bool = False,
     fhi: float | None = None,
+    no_ears: bool = False,
+    back_of_head: bool = False,
+    forehead: bool = False,
+    pics: bool = False,
     code_: str | None = None,
     image_convert: str | None = None,
+    no_post: bool = False,
     threads: float | None = None,
+    force: bool = False,
+    output_format: str | None = None,
+    atlas: str | None = None,
+    expert: str | None = None,
     display_no: float | None = None,
     apply_volume: str | None = None,
     check_volume: InputPathType | None = None,
     check_output_file: InputPathType | None = None,
-    output_format: str | None = None,
     runner: Runner | None = None,
 ) -> MidefaceOutputs:
     """
@@ -363,18 +448,29 @@ def mideface(
         exclusion_mask: Mask to exclude certain regions from defacing.
         samseg_ndilations: Number of dilations for Samseg segmentation.
         samseg_json: JSON configuration for Samseg.
+        samseg_fast: Configure Samseg to run quickly.
+        no_samseg_fast: Do not configure Samseg to run quickly.
         init_reg: Initial registration file for Samseg.
         synthseg_ndilations: Number of dilations for Synthseg segmentation.
         fill_const: Constants for filling regions.
+        fill_zero: Fill regions with zero.
         fhi: FHI value for MRIchangeType().
+        no_ears: Do not include ears in the defacing.
+        back_of_head: Include back of head in defacing.
+        forehead: Include forehead in defacing (risks removing brain).
+        pics: Take pictures of the defaced result.
         code_: Embed code name in pictures.
         image_convert: Path to ImageMagick convert binary for pictures.
+        no_post: Do not make a head surface after defacing.
         threads: Number of threads to use.
+        force: Force reprocessing (only applicable if output directory is used).
+        output_format: Output file format.
+        atlas: Directory containing atlas files.
+        expert: Additional expert options.
         display_no: Xvfb display number for taking pictures.
         apply_volume: Apply midface output to a second volume.
         check_volume: Volume to check if defaced.
         check_output_file: Optional output file for check result.
-        output_format: Output file format.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MidefaceOutputs`).
@@ -389,18 +485,29 @@ def mideface(
         exclusion_mask=exclusion_mask,
         samseg_ndilations=samseg_ndilations,
         samseg_json=samseg_json,
+        samseg_fast=samseg_fast,
+        no_samseg_fast=no_samseg_fast,
         init_reg=init_reg,
         synthseg_ndilations=synthseg_ndilations,
         fill_const=fill_const,
+        fill_zero=fill_zero,
         fhi=fhi,
+        no_ears=no_ears,
+        back_of_head=back_of_head,
+        forehead=forehead,
+        pics=pics,
         code_=code_,
         image_convert=image_convert,
+        no_post=no_post,
         threads=threads,
+        force=force,
+        output_format=output_format,
+        atlas=atlas,
+        expert=expert,
         display_no=display_no,
         apply_volume=apply_volume,
         check_volume=check_volume,
         check_output_file=check_output_file,
-        output_format=output_format,
     )
     return mideface_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mni152reg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MNI152REG_METADATA = Metadata(
-    id="ce57b863d24379ba72442d213f0a02c5cba44366.boutiques",
+    id="8fa95f49688c26996caeccdd18ef44b1edc62d55.boutiques",
     name="mni152reg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -115,7 +115,7 @@ def mni152reg_cargs(
     cargs.append("mni152reg")
     cargs.extend([
         "-s",
-        "-" + params.get("subject")
+        params.get("subject")
     ])
     if params.get("register_1mm"):
         cargs.append("--1")

niwrap_freesurfer/freesurfer/morph_only_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_ONLY_SUBJECT_LH_METADATA = Metadata(
-    id="352935372f9b953d29e77e48bc48053d0bb7123b.boutiques",
+    id="675fa84f456fc1eaf42786b61325807752029a72.boutiques",
     name="morph_only_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -93,9 +93,10 @@ def morph_only_subject_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_only_subject-lh")
     cargs.extend([
         "-lh",
-        "morph_only_subject" + params.get("subject_dir")
+        params.get("subject_dir")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_only_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_ONLY_SUBJECT_RH_METADATA = Metadata(
-    id="cf178313d144b58ca109c79e9c3499855a731ab6.boutiques",
+    id="dfd0ca80bee1df9c17a052f04b511b4001fa744d.boutiques",
     name="morph_only_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -95,9 +95,10 @@ def morph_only_subject_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_only_subject-rh")
     cargs.extend([
         "-rh",
-        "morph_only_subject" + execution.input_file(params.get("subject_dir"))
+        execution.input_file(params.get("subject_dir"))
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_rgb_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_RGB_LH_METADATA = Metadata(
-    id="8a27176b135c7e00506bbb223dc33d4f8b5c331f.boutiques",
+    id="044963f7616c001fb9f232b33ff6dda1d55eaf4f.boutiques",
     name="morph_rgb-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -92,9 +92,10 @@ def morph_rgb_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_rgb-lh")
     cargs.extend([
         "-lh",
-        "morph_rgb" + params.get("subject_id")
+        params.get("subject_id")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_rgb_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_RGB_RH_METADATA = Metadata(
-    id="d9ff451dc5d9779a26edbf9b5422cc9aac7df58e.boutiques",
+    id="aff93e163c0c3d9d9260e950945412279336cdbc.boutiques",
     name="morph_rgb-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def morph_rgb_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_rgb-rh")
     cargs.extend([
         "-rh",
-        "morph_rgb" + params.get("subject_id")
+        params.get("subject_id")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_SUBJECT_LH_METADATA = Metadata(
-    id="da06f833976d33a0c94b485e6e21f58bc7a8916f.boutiques",
+    id="50281e785fbd08bfa132876681fac0d45cfa2be9.boutiques",
     name="morph_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def morph_subject_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_subject-lh")
     cargs.extend([
         "-lh",
-        "morph_subject" + params.get("subject_id")
+        params.get("subject_id")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_SUBJECT_RH_METADATA = Metadata(
-    id="f2d5e549617839220f590599e3a6e8f1eae8c024.boutiques",
+    id="3bc20c9a814d4ed47946818ef81d8f65039baeee.boutiques",
     name="morph_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def morph_subject_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_subject-rh")
     cargs.extend([
         "-rh",
-        "morph_subject" + params.get("subject_id")
+        params.get("subject_id")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/morph_tables_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_TABLES_LH_METADATA = Metadata(
-    id="e50487cf18790588cbef4e2983a79d88589f3cc3.boutiques",
+    id="34324860233ca7709fb6c2b4418a71bd3f0cbdf6.boutiques",
     name="morph_tables-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -98,9 +98,10 @@ def morph_tables_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_tables-lh")
     cargs.extend([
         "-lh",
-        "morph_tables" + execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file"))
     ])
     if params.get("some_flag"):
         cargs.append("--some-flag")