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

niwrap_freesurfer/freesurfer/fs_update.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_UPDATE_METADATA = Metadata(
-    id="4603b7fb31c1aa61646a36fb25725ca6a61d057f.boutiques",
+    id="f55ece15d6ea47dd3edb6a480f7b814dfb337904.boutiques",
     name="fs_update",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,6 +16,8 @@ FS_UPDATE_METADATA = Metadata(
 FsUpdateParameters = typing.TypedDict('FsUpdateParameters', {
     "__STYX_TYPE__": typing.Literal["fs_update"],
     "update_path": typing.NotRequired[str | None],
+    "help_short": bool,
+    "help_medium": bool,
     "help_long": bool,
 })
 
@@ -61,6 +63,8 @@ class FsUpdateOutputs(typing.NamedTuple):
 
 def fs_update_params(
     update_path: str | None = None,
+    help_short: bool = False,
+    help_medium: bool = False,
     help_long: bool = False,
 ) -> FsUpdateParameters:
     """
@@ -69,12 +73,16 @@ def fs_update_params(
     Args:
         update_path: Path to specific files or directories to update, copied\
             recursively.
+        help_short: Show help.
+        help_medium:.
         help_long:.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "fs_update",
+        "help_short": help_short,
+        "help_medium": help_medium,
         "help_long": help_long,
     }
     if update_path is not None:
@@ -99,6 +107,10 @@ def fs_update_cargs(
     cargs.append("fs_update")
     if params.get("update_path") is not None:
         cargs.append(params.get("update_path"))
+    if params.get("help_short"):
+        cargs.append("-h")
+    if params.get("help_medium"):
+        cargs.append("-help")
     if params.get("help_long"):
         cargs.append("--help")
     return cargs
@@ -149,6 +161,8 @@ def fs_update_execute(
 
 def fs_update(
     update_path: str | None = None,
+    help_short: bool = False,
+    help_medium: bool = False,
     help_long: bool = False,
     runner: Runner | None = None,
 ) -> FsUpdateOutputs:
@@ -162,6 +176,8 @@ def fs_update(
     Args:
         update_path: Path to specific files or directories to update, copied\
             recursively.
+        help_short: Show help.
+        help_medium:.
         help_long:.
         runner: Command runner.
     Returns:
@@ -171,6 +187,8 @@ def fs_update(
     execution = runner.start_execution(FS_UPDATE_METADATA)
     params = fs_update_params(
         update_path=update_path,
+        help_short=help_short,
+        help_medium=help_medium,
         help_long=help_long,
     )
     return fs_update_execute(params, execution)

niwrap_freesurfer/freesurfer/fsl_sub_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSL_SUB_MGH_METADATA = Metadata(
-    id="b225e0584e88c37a1a9ef9c5295eb2118fddc2cc.boutiques",
+    id="657f2367434984a9f8159b2c7f6373d5a2b528fc.boutiques",
     name="fsl_sub_mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -213,7 +213,6 @@ def fsl_sub_mgh_cargs(
             "-s",
             params.get("shell_path")
         ])
-    cargs.append("<COMMAND>")
     return cargs
 
 

niwrap_freesurfer/freesurfer/fsr_import.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSR_IMPORT_METADATA = Metadata(
-    id="0f4f0456c8df72ab9210f36b4e8bfb88e6ceba62.boutiques",
+    id="8c46b9370bd04e469266a234c1fd26413c67b9bf.boutiques",
     name="fsr-import",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,6 +16,10 @@ FSR_IMPORT_METADATA = Metadata(
 FsrImportParameters = typing.TypedDict('FsrImportParameters', {
     "__STYX_TYPE__": typing.Literal["fsr-import"],
     "outdir": str,
+    "t1w_input": typing.NotRequired[list[InputPathType] | None],
+    "t2w_input": typing.NotRequired[list[InputPathType] | None],
+    "flair_input": typing.NotRequired[list[InputPathType] | None],
+    "custom_mode_input": typing.NotRequired[list[str] | None],
     "force_update": bool,
     "no_conform": bool,
     "hires": bool,
@@ -72,6 +76,10 @@ class FsrImportOutputs(typing.NamedTuple):
 
 def fsr_import_params(
     outdir: str,
+    t1w_input: list[InputPathType] | None = None,
+    t2w_input: list[InputPathType] | None = None,
+    flair_input: list[InputPathType] | None = None,
+    custom_mode_input: list[str] | None = None,
     force_update: bool = False,
     no_conform: bool = False,
     hires: bool = False,
@@ -81,6 +89,11 @@ def fsr_import_params(
     
     Args:
         outdir: Root directory for output data.
+        t1w_input: Input T1-weighted image files.
+        t2w_input: Input T2-weighted image files.
+        flair_input: Input FLAIR image files.
+        custom_mode_input: Custom modality image file with specified mode name\
+            (not t1w, t2w, or flair).
         force_update: Update files regardless of timestamp.
         no_conform: Do not conform inputs to 1mm, 256 dimensions.
         hires: Same as --no-conform.
@@ -94,6 +107,14 @@ def fsr_import_params(
         "no_conform": no_conform,
         "hires": hires,
     }
+    if t1w_input is not None:
+        params["t1w_input"] = t1w_input
+    if t2w_input is not None:
+        params["t2w_input"] = t2w_input
+    if flair_input is not None:
+        params["flair_input"] = flair_input
+    if custom_mode_input is not None:
+        params["custom_mode_input"] = custom_mode_input
     return params
 
 
@@ -116,10 +137,26 @@ def fsr_import_cargs(
         "--o",
         params.get("outdir")
     ])
-    cargs.append("[T1W...]")
-    cargs.append("[T2W...]")
-    cargs.append("[FLAIR...]")
-    cargs.append("[CUSTOM_MODES...]")
+    if params.get("t1w_input") is not None:
+        cargs.extend([
+            "--t1w",
+            *[execution.input_file(f) for f in params.get("t1w_input")]
+        ])
+    if params.get("t2w_input") is not None:
+        cargs.extend([
+            "--t2w",
+            *[execution.input_file(f) for f in params.get("t2w_input")]
+        ])
+    if params.get("flair_input") is not None:
+        cargs.extend([
+            "--flair",
+            *[execution.input_file(f) for f in params.get("flair_input")]
+        ])
+    if params.get("custom_mode_input") is not None:
+        cargs.extend([
+            "--mode",
+            *params.get("custom_mode_input")
+        ])
     if params.get("force_update"):
         cargs.append("--force-update")
     if params.get("no_conform"):
@@ -178,6 +215,10 @@ def fsr_import_execute(
 
 def fsr_import(
     outdir: str,
+    t1w_input: list[InputPathType] | None = None,
+    t2w_input: list[InputPathType] | None = None,
+    flair_input: list[InputPathType] | None = None,
+    custom_mode_input: list[str] | None = None,
     force_update: bool = False,
     no_conform: bool = False,
     hires: bool = False,
@@ -192,6 +233,11 @@ def fsr_import(
     
     Args:
         outdir: Root directory for output data.
+        t1w_input: Input T1-weighted image files.
+        t2w_input: Input T2-weighted image files.
+        flair_input: Input FLAIR image files.
+        custom_mode_input: Custom modality image file with specified mode name\
+            (not t1w, t2w, or flair).
         force_update: Update files regardless of timestamp.
         no_conform: Do not conform inputs to 1mm, 256 dimensions.
         hires: Same as --no-conform.
@@ -203,6 +249,10 @@ def fsr_import(
     execution = runner.start_execution(FSR_IMPORT_METADATA)
     params = fsr_import_params(
         outdir=outdir,
+        t1w_input=t1w_input,
+        t2w_input=t2w_input,
+        flair_input=flair_input,
+        custom_mode_input=custom_mode_input,
         force_update=force_update,
         no_conform=no_conform,
         hires=hires,

niwrap_freesurfer/freesurfer/fvcompare.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FVCOMPARE_METADATA = Metadata(
-    id="84e27ef54cc73075db70cca3ebbdd40631c9472d.boutiques",
+    id="34ef4943d85118cb4252e43061bab2f274dff0b4.boutiques",
     name="fvcompare",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -26,6 +26,7 @@ FvcompareParameters = typing.TypedDict('FvcompareParameters', {
     "segmentation": typing.NotRequired[str | None],
     "aseg": bool,
     "no_seg": bool,
+    "left_hemi": bool,
     "right_hemi": bool,
     "no_surf": bool,
     "gray_levels": typing.NotRequired[list[float] | None],
@@ -93,6 +94,7 @@ def fvcompare_params(
     segmentation: str | None = None,
     aseg: bool = False,
     no_seg: bool = False,
+    left_hemi: bool = False,
     right_hemi: bool = False,
     no_surf: bool = False,
     gray_levels: list[float] | None = None,
@@ -124,6 +126,7 @@ def fvcompare_params(
             aparc+aseg.mgz, can have multiple).
         aseg: Add aseg.mgz to segmentation list.
         no_seg: Do not display segmentations.
+        left_hemi: Only display left hemisphere.
         right_hemi: Only display right hemisphere.
         no_surf: Do not display surfaces.
         gray_levels: Set gray scale levels.
@@ -147,6 +150,7 @@ def fvcompare_params(
         "subject2": subject2,
         "aseg": aseg,
         "no_seg": no_seg,
+        "left_hemi": left_hemi,
         "right_hemi": right_hemi,
         "no_surf": no_surf,
         "aparc": aparc,
@@ -246,6 +250,8 @@ def fvcompare_cargs(
         cargs.append("--aseg")
     if params.get("no_seg"):
         cargs.append("--no-seg")
+    if params.get("left_hemi"):
+        cargs.append("--lh")
     if params.get("right_hemi"):
         cargs.append("--rh")
     if params.get("no_surf"):
@@ -349,6 +355,7 @@ def fvcompare(
     segmentation: str | None = None,
     aseg: bool = False,
     no_seg: bool = False,
+    left_hemi: bool = False,
     right_hemi: bool = False,
     no_surf: bool = False,
     gray_levels: list[float] | None = None,
@@ -386,6 +393,7 @@ def fvcompare(
             aparc+aseg.mgz, can have multiple).
         aseg: Add aseg.mgz to segmentation list.
         no_seg: Do not display segmentations.
+        left_hemi: Only display left hemisphere.
         right_hemi: Only display right hemisphere.
         no_surf: Do not display surfaces.
         gray_levels: Set gray scale levels.
@@ -418,6 +426,7 @@ def fvcompare(
         segmentation=segmentation,
         aseg=aseg,
         no_seg=no_seg,
+        left_hemi=left_hemi,
         right_hemi=right_hemi,
         no_surf=no_surf,
         gray_levels=gray_levels,

niwrap_freesurfer/freesurfer/gca_apply.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GCA_APPLY_METADATA = Metadata(
-    id="004863971f906d9a0b7892c9101381a0f012a5c2.boutiques",
+    id="37d628d973685edc2921052f548a797e0b449eb8.boutiques",
     name="gca-apply",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -182,9 +182,10 @@ def gca_apply_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("gca-apply")
     cargs.extend([
         "-apply",
-        "gca" + execution.input_file(params.get("gcafile"))
+        execution.input_file(params.get("gcafile"))
     ])
     cargs.append(params.get("subject"))
     if params.get("nthreads") is not None:

niwrap_freesurfer/freesurfer/gdcmconv_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GDCMCONV_FS_METADATA = Metadata(
-    id="c4cb69979a329deef98f15b2e797b9c57375a6ef.boutiques",
+    id="98f7b1994832a771c3433368967176f42a435bc4.boutiques",
     name="gdcmconv.fs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -261,7 +261,7 @@ def gdcmconv_fs_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("gdcmconv")
+    cargs.append("gdcmconv.fs")
     cargs.append(execution.input_file(params.get("input_file")))
     cargs.append(params.get("output_file"))
     if params.get("explicit_flag"):

niwrap_freesurfer/freesurfer/get_label_thickness.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GET_LABEL_THICKNESS_METADATA = Metadata(
-    id="dee540c5d6addffa9eea35a7fd1572afd491a587.boutiques",
+    id="f6297b36ddfbae019c6113cbf899ac43a825fe9b.boutiques",
     name="get_label_thickness",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -92,7 +92,6 @@ def get_label_thickness_cargs(
     cargs = []
     cargs.append("get_label_thickness")
     cargs.append(execution.input_file(params.get("infile")))
-    cargs.append("[OPTIONS]")
     return cargs
 
 

niwrap_freesurfer/freesurfer/groupstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GROUPSTATS_METADATA = Metadata(
-    id="b3ed2b7c0070683b40d589d0c64dbdd96b53715f.boutiques",
+    id="355e1a7428f21999fd48f18935d2d56917a02e73.boutiques",
     name="groupstats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,11 +16,21 @@ GROUPSTATS_METADATA = Metadata(
 GroupstatsParameters = typing.TypedDict('GroupstatsParameters', {
     "__STYX_TYPE__": typing.Literal["groupstats"],
     "outdir": str,
+    "group_fsgd": typing.NotRequired[InputPathType | None],
     "subjectfile": typing.NotRequired[InputPathType | None],
     "fwhm": typing.NotRequired[list[float] | None],
     "subject_dir": typing.NotRequired[str | None],
     "mapname": typing.NotRequired[str | None],
     "srcsurfreg": typing.NotRequired[str | None],
+    "no_maps": bool,
+    "lh_only": bool,
+    "rh_only": bool,
+    "no_aparcstats": bool,
+    "no_asegstats": bool,
+    "no_wparcstats": bool,
+    "no_stats": bool,
+    "new": bool,
+    "base": bool,
     "keep53": bool,
 })
 
@@ -69,11 +79,21 @@ class GroupstatsOutputs(typing.NamedTuple):
 
 def groupstats_params(
     outdir: str,
+    group_fsgd: InputPathType | None = None,
     subjectfile: InputPathType | None = None,
     fwhm: list[float] | None = None,
     subject_dir: str | None = None,
     mapname: str | None = None,
     srcsurfreg: str | None = None,
+    no_maps: bool = False,
+    lh_only: bool = False,
+    rh_only: bool = False,
+    no_aparcstats: bool = False,
+    no_asegstats: bool = False,
+    no_wparcstats: bool = False,
+    no_stats: bool = False,
+    new: bool = False,
+    base: bool = False,
     keep53: bool = False,
 ) -> GroupstatsParameters:
     """
@@ -81,11 +101,22 @@ def groupstats_params(
     
     Args:
         outdir: Output folder.
+        group_fsgd: Specify the FSGD file for the group.
         subjectfile: Subject list file.
         fwhm: Specify smoothing level(s).
         subject_dir: Subject directory.
         mapname: Use the given map name.
         srcsurfreg: Source surface registration (default is sphere.reg).
+        no_maps: Only analyze ROI data.
+        lh_only: Only analyze left hemisphere.
+        rh_only: Only analyze right hemisphere.
+        no_aparcstats: Do not compute aparcstats.
+        no_asegstats: Do not compute asegstats.
+        no_wparcstats: Do not compute wmparcstats.
+        no_stats: Do not perform any ROI stats.
+        new: Append .new.mris_make_surfaces to map names.
+        base: Sets measure thickness area volume curvature sulcus (excludes\
+            white-gray percentage).
         keep53: Keep 5.3 aseg names (e.g., Thalamus-Proper).
     Returns:
         Parameter dictionary
@@ -93,8 +124,19 @@ def groupstats_params(
     params = {
         "__STYXTYPE__": "groupstats",
         "outdir": outdir,
+        "no_maps": no_maps,
+        "lh_only": lh_only,
+        "rh_only": rh_only,
+        "no_aparcstats": no_aparcstats,
+        "no_asegstats": no_asegstats,
+        "no_wparcstats": no_wparcstats,
+        "no_stats": no_stats,
+        "new": new,
+        "base": base,
         "keep53": keep53,
     }
+    if group_fsgd is not None:
+        params["group_fsgd"] = group_fsgd
     if subjectfile is not None:
         params["subjectfile"] = subjectfile
     if fwhm is not None:
@@ -127,6 +169,11 @@ def groupstats_cargs(
         "--o",
         params.get("outdir")
     ])
+    if params.get("group_fsgd") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("group_fsgd"))
+        ])
     if params.get("subjectfile") is not None:
         cargs.extend([
             "--f",
@@ -152,6 +199,24 @@ def groupstats_cargs(
             "--srcsurfreg",
             params.get("srcsurfreg")
         ])
+    if params.get("no_maps"):
+        cargs.append("--no-maps")
+    if params.get("lh_only"):
+        cargs.append("--lh")
+    if params.get("rh_only"):
+        cargs.append("--rh")
+    if params.get("no_aparcstats"):
+        cargs.append("--no-aparcstats")
+    if params.get("no_asegstats"):
+        cargs.append("--no-asegstats")
+    if params.get("no_wparcstats"):
+        cargs.append("--no-wparcstats")
+    if params.get("no_stats"):
+        cargs.append("--no-stats")
+    if params.get("new"):
+        cargs.append("--new")
+    if params.get("base"):
+        cargs.append("--base")
     if params.get("keep53"):
         cargs.append("--keep53")
     return cargs
@@ -204,11 +269,21 @@ def groupstats_execute(
 
 def groupstats(
     outdir: str,
+    group_fsgd: InputPathType | None = None,
     subjectfile: InputPathType | None = None,
     fwhm: list[float] | None = None,
     subject_dir: str | None = None,
     mapname: str | None = None,
     srcsurfreg: str | None = None,
+    no_maps: bool = False,
+    lh_only: bool = False,
+    rh_only: bool = False,
+    no_aparcstats: bool = False,
+    no_asegstats: bool = False,
+    no_wparcstats: bool = False,
+    no_stats: bool = False,
+    new: bool = False,
+    base: bool = False,
     keep53: bool = False,
     runner: Runner | None = None,
 ) -> GroupstatsOutputs:
@@ -222,11 +297,22 @@ def groupstats(
     
     Args:
         outdir: Output folder.
+        group_fsgd: Specify the FSGD file for the group.
         subjectfile: Subject list file.
         fwhm: Specify smoothing level(s).
         subject_dir: Subject directory.
         mapname: Use the given map name.
         srcsurfreg: Source surface registration (default is sphere.reg).
+        no_maps: Only analyze ROI data.
+        lh_only: Only analyze left hemisphere.
+        rh_only: Only analyze right hemisphere.
+        no_aparcstats: Do not compute aparcstats.
+        no_asegstats: Do not compute asegstats.
+        no_wparcstats: Do not compute wmparcstats.
+        no_stats: Do not perform any ROI stats.
+        new: Append .new.mris_make_surfaces to map names.
+        base: Sets measure thickness area volume curvature sulcus (excludes\
+            white-gray percentage).
         keep53: Keep 5.3 aseg names (e.g., Thalamus-Proper).
         runner: Command runner.
     Returns:
@@ -236,11 +322,21 @@ def groupstats(
     execution = runner.start_execution(GROUPSTATS_METADATA)
     params = groupstats_params(
         outdir=outdir,
+        group_fsgd=group_fsgd,
         subjectfile=subjectfile,
         fwhm=fwhm,
         subject_dir=subject_dir,
         mapname=mapname,
         srcsurfreg=srcsurfreg,
+        no_maps=no_maps,
+        lh_only=lh_only,
+        rh_only=rh_only,
+        no_aparcstats=no_aparcstats,
+        no_asegstats=no_asegstats,
+        no_wparcstats=no_wparcstats,
+        no_stats=no_stats,
+        new=new,
+        base=base,
         keep53=keep53,
     )
     return groupstats_execute(params, execution)

niwrap_freesurfer/freesurfer/groupstatsdiff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GROUPSTATSDIFF_METADATA = Metadata(
-    id="474a0a73a03ccd5e8c25186fbb8a8f0ccde75dd7.boutiques",
+    id="fd778211449d90ec41caacb3a7dc64cdb74d5085.boutiques",
     name="groupstatsdiff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -177,15 +177,15 @@ def groupstatsdiff_cargs(
     cargs.append("groupstatsdiff")
     cargs.extend([
         "-g1",
-        "-" + params.get("group1_dir")
+        params.get("group1_dir")
     ])
     cargs.extend([
         "-g2",
-        "-" + params.get("group2_dir")
+        params.get("group2_dir")
     ])
     cargs.extend([
         "-o",
-        "-" + params.get("output_dir")
+        params.get("output_dir")
     ])
     if params.get("no_maps"):
         cargs.append("--no-maps")

niwrap_freesurfer/freesurfer/hiam_make_surfaces.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HIAM_MAKE_SURFACES_METADATA = Metadata(
-    id="eedce2967ed9d851c796ec7ce683d74d056d3684.boutiques",
+    id="1b161d9791e99b79bc12c2e006b7a1a47156fb9f.boutiques",
     name="hiam_make_surfaces",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -96,7 +96,6 @@ def hiam_make_surfaces_cargs(
     """
     cargs = []
     cargs.append("hiam_make_surfaces")
-    cargs.append("[OPTIONS]")
     cargs.append(params.get("subject_name"))
     cargs.append(params.get("structure"))
     return cargs

niwrap_freesurfer/freesurfer/histo_synthesize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HISTO_SYNTHESIZE_METADATA = Metadata(
-    id="ebfa527b23cadea769992b1ad756ebe6c1f58512.boutiques",
+    id="7ba52ad8ca54fc771c31d5fba965b50932dba8fe.boutiques",
     name="histo_synthesize",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -102,7 +102,6 @@ def histo_synthesize_cargs(
     """
     cargs = []
     cargs.append("histo_synthesize")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("mri_volume")))
     cargs.append(execution.input_file(params.get("histo_volume")))
     cargs.append(params.get("synthetic_histo"))

niwrap_freesurfer/freesurfer/inflate_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_LH_METADATA = Metadata(
-    id="13f58b307e30c9d1d7c23e3d8eda03727c68266d.boutiques",
+    id="941fff4146cba765ed908e2c762f2faabcdf05c1.boutiques",
     name="inflate_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -94,9 +94,10 @@ def inflate_subject_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("inflate_subject-lh")
     cargs.extend([
         "-lh",
-        "inflate_subject" + params.get("input_folder")
+        params.get("input_folder")
     ])
     if params.get("hostname_flag"):
         cargs.append("hostname")

niwrap_freesurfer/freesurfer/inflate_subject_new_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_NEW_LH_METADATA = Metadata(
-    id="08307c12a50c2ff8603980e07c1bcf6e9a16f2e1.boutiques",
+    id="2e5d93e0cd0ec7e2b630ed81133b9ac7aefe52f9.boutiques",
     name="inflate_subject_new-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -93,11 +93,11 @@ def inflate_subject_new_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("inflate_subject_new")
     cargs.extend([
         "-lh",
-        "inflate_subject_new" + params.get("subject_dir")
+        params.get("subject_dir")
     ])
-    cargs.append("[OPTIONS]")
     return cargs
 
 

niwrap_freesurfer/freesurfer/inflate_subject_new_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_NEW_RH_METADATA = Metadata(
-    id="6ededf15eee0d58308af964a359eb602b1b300a0.boutiques",
+    id="3037b7690756cae99cf0b6e186eebe74d51160c7.boutiques",
     name="inflate_subject_new-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -91,10 +91,11 @@ def inflate_subject_new_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("inflate_subject_new-rh")
     if params.get("args") is not None:
         cargs.extend([
             "-rh",
-            "inflate_subject_new" + params.get("args")
+            params.get("args")
         ])
     return cargs