niwrap-freesurfer 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DIFF_METADATA = Metadata(
-    id="30172af00f20644762a6e2ce032311fb482cfc14.boutiques",
+    id="8cd3b28eed03b89b73b4ad8e6f6e7309b348546c.boutiques",
     name="mris_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -22,6 +22,28 @@ MrisDiffParameters = typing.TypedDict('MrisDiffParameters', {
     "subj_dir1": typing.NotRequired[str | None],
     "subj_dir2": typing.NotRequired[str | None],
     "hemisphere": str,
+    "surf": typing.NotRequired[str | None],
+    "curv": typing.NotRequired[str | None],
+    "aparc": typing.NotRequired[str | None],
+    "aparc2": typing.NotRequired[str | None],
+    "simple": bool,
+    "simple_patch": bool,
+    "thresh": typing.NotRequired[float | None],
+    "maxerrs": typing.NotRequired[float | None],
+    "renumbered": bool,
+    "worst_bucket": typing.NotRequired[str | None],
+    "grid": typing.NotRequired[str | None],
+    "no_check_xyz": bool,
+    "no_check_nxyz": bool,
+    "xyz_rms": typing.NotRequired[str | None],
+    "angle_rms": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[float | None],
+    "min_dist": typing.NotRequired[str | None],
+    "debug": bool,
+    "gdiag_no": typing.NotRequired[float | None],
+    "check_opts": bool,
+    "help": bool,
+    "version": bool,
 })
 
 
@@ -72,6 +94,28 @@ def mris_diff_params(
     hemisphere: str,
     subj_dir1: str | None = None,
     subj_dir2: str | None = None,
+    surf: str | None = None,
+    curv: str | None = None,
+    aparc: str | None = None,
+    aparc2: str | None = None,
+    simple: bool = False,
+    simple_patch: bool = False,
+    thresh: float | None = None,
+    maxerrs: float | None = None,
+    renumbered: bool = False,
+    worst_bucket: str | None = None,
+    grid: str | None = None,
+    no_check_xyz: bool = False,
+    no_check_nxyz: bool = False,
+    xyz_rms: str | None = None,
+    angle_rms: str | None = None,
+    seed: float | None = None,
+    min_dist: str | None = None,
+    debug: bool = False,
+    gdiag_no: float | None = None,
+    check_opts: bool = False,
+    help_: bool = False,
+    version: bool = False,
 ) -> MrisDiffParameters:
     """
     Build parameters.
@@ -84,6 +128,30 @@ def mris_diff_params(
         hemisphere: Hemisphere (rh or lh).
         subj_dir1: Directory for Subject 1 (default is SUBJECTS_DIR).
         subj_dir2: Directory for Subject 2 (default is SUBJECTS_DIR).
+        surf: Compare surface.
+        curv: Compare curvature.
+        aparc: Compare aparc annotation.
+        aparc2: Optional different name to compare to aparc.
+        simple: Simple comparison of two surfaces to just report differences.
+        simple_patch: Simple comparison of two patches.
+        thresh: Threshold (default=0) [Note: Not currently implemented!].
+        maxerrs: Stop looping after N errors (default=10).
+        renumbered: Vertices or faces may have been renumbered and a few\
+            deleted.
+        worst_bucket: Compute the worst histogram bucket each vertex is in.
+        grid: Label the vertices of edges that span a grid based on the\
+            provided spacing float.
+        no_check_xyz: Do not check vertex xyz.
+        no_check_nxyz: Do not check vertex normals.
+        xyz_rms: Compute and save RMS diff between xyz.
+        angle_rms: Compute angle on sphere between xyz.
+        seed: Set random seed for degenerate normals.
+        min_dist: Compute vertex-by-vertex RMS distance between surfaces.
+        debug: Enable debugging output.
+        gdiag_no: Specify Gdiag_no.
+        check_opts: Only check options and exit.
+        help_: Display help information.
+        version: Display version information.
     Returns:
         Parameter dictionary
     """
@@ -94,11 +162,46 @@ def mris_diff_params(
         "subject1": subject1,
         "subject2": subject2,
         "hemisphere": hemisphere,
+        "simple": simple,
+        "simple_patch": simple_patch,
+        "renumbered": renumbered,
+        "no_check_xyz": no_check_xyz,
+        "no_check_nxyz": no_check_nxyz,
+        "debug": debug,
+        "check_opts": check_opts,
+        "help": help_,
+        "version": version,
     }
     if subj_dir1 is not None:
         params["subj_dir1"] = subj_dir1
     if subj_dir2 is not None:
         params["subj_dir2"] = subj_dir2
+    if surf is not None:
+        params["surf"] = surf
+    if curv is not None:
+        params["curv"] = curv
+    if aparc is not None:
+        params["aparc"] = aparc
+    if aparc2 is not None:
+        params["aparc2"] = aparc2
+    if thresh is not None:
+        params["thresh"] = thresh
+    if maxerrs is not None:
+        params["maxerrs"] = maxerrs
+    if worst_bucket is not None:
+        params["worst_bucket"] = worst_bucket
+    if grid is not None:
+        params["grid"] = grid
+    if xyz_rms is not None:
+        params["xyz_rms"] = xyz_rms
+    if angle_rms is not None:
+        params["angle_rms"] = angle_rms
+    if seed is not None:
+        params["seed"] = seed
+    if min_dist is not None:
+        params["min_dist"] = min_dist
+    if gdiag_no is not None:
+        params["gdiag_no"] = gdiag_no
     return params
 
 
@@ -141,6 +244,89 @@ def mris_diff_cargs(
         "--hemi",
         params.get("hemisphere")
     ])
+    if params.get("surf") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surf")
+        ])
+    if params.get("curv") is not None:
+        cargs.extend([
+            "--curv",
+            params.get("curv")
+        ])
+    if params.get("aparc") is not None:
+        cargs.extend([
+            "--aparc",
+            params.get("aparc")
+        ])
+    if params.get("aparc2") is not None:
+        cargs.extend([
+            "--aparc2",
+            params.get("aparc2")
+        ])
+    if params.get("simple"):
+        cargs.append("--simple")
+    if params.get("simple_patch"):
+        cargs.append("--simple-patch")
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "--thresh",
+            str(params.get("thresh"))
+        ])
+    if params.get("maxerrs") is not None:
+        cargs.extend([
+            "--maxerrs",
+            str(params.get("maxerrs"))
+        ])
+    if params.get("renumbered"):
+        cargs.append("--renumbered")
+    if params.get("worst_bucket") is not None:
+        cargs.extend([
+            "--worst-bucket",
+            params.get("worst_bucket")
+        ])
+    if params.get("grid") is not None:
+        cargs.extend([
+            "--grid",
+            params.get("grid")
+        ])
+    if params.get("no_check_xyz"):
+        cargs.append("--no-check-xyz")
+    if params.get("no_check_nxyz"):
+        cargs.append("--no-check-nxyz")
+    if params.get("xyz_rms") is not None:
+        cargs.extend([
+            "--xyz-rms",
+            params.get("xyz_rms")
+        ])
+    if params.get("angle_rms") is not None:
+        cargs.extend([
+            "--angle-rms",
+            params.get("angle_rms")
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("seed"))
+        ])
+    if params.get("min_dist") is not None:
+        cargs.extend([
+            "--min-dist",
+            params.get("min_dist")
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("gdiag_no") is not None:
+        cargs.extend([
+            "--gdiag_no",
+            str(params.get("gdiag_no"))
+        ])
+    if params.get("check_opts"):
+        cargs.append("--checkopts")
+    if params.get("help"):
+        cargs.append("--help")
+    if params.get("version"):
+        cargs.append("--version")
     return cargs
 
 
@@ -195,6 +381,28 @@ def mris_diff(
     hemisphere: str,
     subj_dir1: str | None = None,
     subj_dir2: str | None = None,
+    surf: str | None = None,
+    curv: str | None = None,
+    aparc: str | None = None,
+    aparc2: str | None = None,
+    simple: bool = False,
+    simple_patch: bool = False,
+    thresh: float | None = None,
+    maxerrs: float | None = None,
+    renumbered: bool = False,
+    worst_bucket: str | None = None,
+    grid: str | None = None,
+    no_check_xyz: bool = False,
+    no_check_nxyz: bool = False,
+    xyz_rms: str | None = None,
+    angle_rms: str | None = None,
+    seed: float | None = None,
+    min_dist: str | None = None,
+    debug: bool = False,
+    gdiag_no: float | None = None,
+    check_opts: bool = False,
+    help_: bool = False,
+    version: bool = False,
     runner: Runner | None = None,
 ) -> MrisDiffOutputs:
     """
@@ -212,6 +420,30 @@ def mris_diff(
         hemisphere: Hemisphere (rh or lh).
         subj_dir1: Directory for Subject 1 (default is SUBJECTS_DIR).
         subj_dir2: Directory for Subject 2 (default is SUBJECTS_DIR).
+        surf: Compare surface.
+        curv: Compare curvature.
+        aparc: Compare aparc annotation.
+        aparc2: Optional different name to compare to aparc.
+        simple: Simple comparison of two surfaces to just report differences.
+        simple_patch: Simple comparison of two patches.
+        thresh: Threshold (default=0) [Note: Not currently implemented!].
+        maxerrs: Stop looping after N errors (default=10).
+        renumbered: Vertices or faces may have been renumbered and a few\
+            deleted.
+        worst_bucket: Compute the worst histogram bucket each vertex is in.
+        grid: Label the vertices of edges that span a grid based on the\
+            provided spacing float.
+        no_check_xyz: Do not check vertex xyz.
+        no_check_nxyz: Do not check vertex normals.
+        xyz_rms: Compute and save RMS diff between xyz.
+        angle_rms: Compute angle on sphere between xyz.
+        seed: Set random seed for degenerate normals.
+        min_dist: Compute vertex-by-vertex RMS distance between surfaces.
+        debug: Enable debugging output.
+        gdiag_no: Specify Gdiag_no.
+        check_opts: Only check options and exit.
+        help_: Display help information.
+        version: Display version information.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDiffOutputs`).
@@ -226,6 +458,28 @@ def mris_diff(
         subj_dir1=subj_dir1,
         subj_dir2=subj_dir2,
         hemisphere=hemisphere,
+        surf=surf,
+        curv=curv,
+        aparc=aparc,
+        aparc2=aparc2,
+        simple=simple,
+        simple_patch=simple_patch,
+        thresh=thresh,
+        maxerrs=maxerrs,
+        renumbered=renumbered,
+        worst_bucket=worst_bucket,
+        grid=grid,
+        no_check_xyz=no_check_xyz,
+        no_check_nxyz=no_check_nxyz,
+        xyz_rms=xyz_rms,
+        angle_rms=angle_rms,
+        seed=seed,
+        min_dist=min_dist,
+        debug=debug,
+        gdiag_no=gdiag_no,
+        check_opts=check_opts,
+        help_=help_,
+        version=version,
     )
     return mris_diff_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mris_distance_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DISTANCE_MAP_METADATA = Metadata(
-    id="3d8e889c4b656344736f94614b767e1d77d78242.boutiques",
+    id="686ff961ac8e9db74639a1364b1f5b20b600667e.boutiques",
     name="mris_distance_map",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -98,7 +98,6 @@ def mris_distance_map_cargs(
     """
     cargs = []
     cargs.append("mris_distance_map")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_surface_file")))
     cargs.append(params.get("output_scalar_field"))
     return cargs

niwrap_freesurfer/freesurfer/mris_errors.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ERRORS_METADATA = Metadata(
-    id="ef9b47e313219e97d7f5d816c34ec14bc6f35660.boutiques",
+    id="84c4666dcea46df17569c6e5d435ebf2cb451d60.boutiques",
     name="mris_errors",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -91,7 +91,6 @@ def mris_errors_cargs(
     """
     cargs = []
     cargs.append("mris_errors")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_image_file")))
     return cargs
 

niwrap_freesurfer/freesurfer/mris_info.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_INFO_METADATA = Metadata(
-    id="f8473bd4b6a90f8c8b3dbe8a7c1e45f9016b4d73.boutiques",
+    id="8c4d52b8480a8839ff1677fa53139a6b9fbea64a.boutiques",
     name="mris_info",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,23 +18,23 @@ MrisInfoParameters = typing.TypedDict('MrisInfoParameters', {
     "surfacefile": InputPathType,
     "outfile": typing.NotRequired[InputPathType | None],
     "subject_hemi_surfname": typing.NotRequired[str | None],
+    "talairach_xfm_flag": bool,
+    "rescale_flag": bool,
     "patchfile": typing.NotRequired[InputPathType | None],
     "vertex_number": typing.NotRequired[float | None],
     "extended_vertex_number": typing.NotRequired[float | None],
     "curvfile": typing.NotRequired[InputPathType | None],
     "annotfile": typing.NotRequired[InputPathType | None],
+    "area_stats_flag": bool,
     "edge_stats_id": typing.NotRequired[str | None],
     "edge_number": typing.NotRequired[float | None],
     "vtxno": typing.NotRequired[str | None],
     "matrix_format": typing.NotRequired[str | None],
+    "quality_stats_flag": bool,
+    "intersections_flag": bool,
     "mask_file": typing.NotRequired[InputPathType | None],
     "label_file": typing.NotRequired[InputPathType | None],
     "edge_file": typing.NotRequired[InputPathType | None],
-    "talairach_xfm_flag": bool,
-    "rescale_flag": bool,
-    "area_stats_flag": bool,
-    "quality_stats_flag": bool,
-    "intersections_flag": bool,
     "nogifti_flag": bool,
     "version_flag": bool,
     "help_flag": bool,
@@ -89,23 +89,23 @@ def mris_info_params(
     surfacefile: InputPathType,
     outfile: InputPathType | None = None,
     subject_hemi_surfname: str | None = None,
+    talairach_xfm_flag: bool = False,
+    rescale_flag: bool = False,
     patchfile: InputPathType | None = None,
     vertex_number: float | None = None,
     extended_vertex_number: float | None = None,
     curvfile: InputPathType | None = None,
     annotfile: InputPathType | None = None,
+    area_stats_flag: bool = False,
     edge_stats_id: str | None = None,
     edge_number: float | None = None,
     vtxno: str | None = None,
     matrix_format: str | None = None,
+    quality_stats_flag: bool = False,
+    intersections_flag: bool = False,
     mask_file: InputPathType | None = None,
     label_file: InputPathType | None = None,
     edge_file: InputPathType | None = None,
-    talairach_xfm_flag: bool = False,
-    rescale_flag: bool = False,
-    area_stats_flag: bool = False,
-    quality_stats_flag: bool = False,
-    intersections_flag: bool = False,
     nogifti_flag: bool = False,
     version_flag: bool = False,
     help_flag: bool = False,
@@ -117,6 +117,8 @@ def mris_info_params(
         surfacefile: Surface file to process.
         outfile: Save some data to outfile.
         subject_hemi_surfname: Instead of surfacefile.
+        talairach_xfm_flag: Apply talairach xfm before reporting info.
+        rescale_flag: Rescale group surface to match average metrics.
         patchfile: Load patch before reporting.
         vertex_number: Print out vertex information for vertex vnum.
         extended_vertex_number: Print out extended vertex information for\
@@ -124,21 +126,19 @@ def mris_info_params(
         curvfile: Check if curvature file vertices match surface vertices.
         annotfile: Check if annotation file vertices match surface vertices;\
             dump colortable.
+        area_stats_flag: Compute stats on triangle area (n, mean, std, min,\
+            max).
         edge_stats_id: Compute stats on edge metric (n, mean, std, min, max);\
             id=0=length, id=1=dot, id=2=angle, id<0= all.
         edge_number: Print out extended information about edge.
         vtxno: Write Matlab file to plot vertex neighborhood.
         matrix_format: Set format for matrix printing (e.g., %12.8f).
-        mask_file: Only compute edge and area stats using vertices in mask.
-        label_file: Only compute edge and area stats using vertices in label.
-        edge_file: Print edge info for all edges into file.
-        talairach_xfm_flag: Apply talairach xfm before reporting info.
-        rescale_flag: Rescale group surface to match average metrics.
-        area_stats_flag: Compute stats on triangle area (n, mean, std, min,\
-            max).
         quality_stats_flag: Print out surface quality stats.
         intersections_flag: Print the number of vertices that belong to a face\
             that intersects another face.
+        mask_file: Only compute edge and area stats using vertices in mask.
+        label_file: Only compute edge and area stats using vertices in label.
+        edge_file: Print edge info for all edges into file.
         nogifti_flag: No dump of GIFTI struct, read .gii as surface instead.
         version_flag: Print version and exits.
         help_flag: No clue what this does.
@@ -214,6 +214,10 @@ def mris_info_cargs(
             "--s",
             params.get("subject_hemi_surfname")
         ])
+    if params.get("talairach_xfm_flag"):
+        cargs.append("--t")
+    if params.get("rescale_flag"):
+        cargs.append("--r")
     if params.get("patchfile") is not None:
         cargs.extend([
             "--patch",
@@ -239,6 +243,8 @@ def mris_info_cargs(
             "--a",
             execution.input_file(params.get("annotfile"))
         ])
+    if params.get("area_stats_flag"):
+        cargs.append("--area-stats")
     if params.get("edge_stats_id") is not None:
         cargs.extend([
             "--edge-stats",
@@ -259,6 +265,10 @@ def mris_info_cargs(
             "--mtx-fmt",
             params.get("matrix_format")
         ])
+    if params.get("quality_stats_flag"):
+        cargs.append("--quality")
+    if params.get("intersections_flag"):
+        cargs.append("--intersections")
     if params.get("mask_file") is not None:
         cargs.extend([
             "--mask",
@@ -274,17 +284,6 @@ def mris_info_cargs(
             "--edge-file",
             execution.input_file(params.get("edge_file"))
         ])
-    if params.get("talairach_xfm_flag"):
-        cargs.append("--t")
-    if params.get("rescale_flag"):
-        cargs.append("--r")
-    if params.get("area_stats_flag"):
-        cargs.append("--area-stats")
-    cargs.append("[EDGE_STATS_FLAG]")
-    if params.get("quality_stats_flag"):
-        cargs.append("--quality")
-    if params.get("intersections_flag"):
-        cargs.append("--intersections")
     if params.get("nogifti_flag"):
         cargs.append("--nogifti-disp-image")
     if params.get("version_flag"):
@@ -343,23 +342,23 @@ def mris_info(
     surfacefile: InputPathType,
     outfile: InputPathType | None = None,
     subject_hemi_surfname: str | None = None,
+    talairach_xfm_flag: bool = False,
+    rescale_flag: bool = False,
     patchfile: InputPathType | None = None,
     vertex_number: float | None = None,
     extended_vertex_number: float | None = None,
     curvfile: InputPathType | None = None,
     annotfile: InputPathType | None = None,
+    area_stats_flag: bool = False,
     edge_stats_id: str | None = None,
     edge_number: float | None = None,
     vtxno: str | None = None,
     matrix_format: str | None = None,
+    quality_stats_flag: bool = False,
+    intersections_flag: bool = False,
     mask_file: InputPathType | None = None,
     label_file: InputPathType | None = None,
     edge_file: InputPathType | None = None,
-    talairach_xfm_flag: bool = False,
-    rescale_flag: bool = False,
-    area_stats_flag: bool = False,
-    quality_stats_flag: bool = False,
-    intersections_flag: bool = False,
     nogifti_flag: bool = False,
     version_flag: bool = False,
     help_flag: bool = False,
@@ -376,6 +375,8 @@ def mris_info(
         surfacefile: Surface file to process.
         outfile: Save some data to outfile.
         subject_hemi_surfname: Instead of surfacefile.
+        talairach_xfm_flag: Apply talairach xfm before reporting info.
+        rescale_flag: Rescale group surface to match average metrics.
         patchfile: Load patch before reporting.
         vertex_number: Print out vertex information for vertex vnum.
         extended_vertex_number: Print out extended vertex information for\
@@ -383,21 +384,19 @@ def mris_info(
         curvfile: Check if curvature file vertices match surface vertices.
         annotfile: Check if annotation file vertices match surface vertices;\
             dump colortable.
+        area_stats_flag: Compute stats on triangle area (n, mean, std, min,\
+            max).
         edge_stats_id: Compute stats on edge metric (n, mean, std, min, max);\
             id=0=length, id=1=dot, id=2=angle, id<0= all.
         edge_number: Print out extended information about edge.
         vtxno: Write Matlab file to plot vertex neighborhood.
         matrix_format: Set format for matrix printing (e.g., %12.8f).
-        mask_file: Only compute edge and area stats using vertices in mask.
-        label_file: Only compute edge and area stats using vertices in label.
-        edge_file: Print edge info for all edges into file.
-        talairach_xfm_flag: Apply talairach xfm before reporting info.
-        rescale_flag: Rescale group surface to match average metrics.
-        area_stats_flag: Compute stats on triangle area (n, mean, std, min,\
-            max).
         quality_stats_flag: Print out surface quality stats.
         intersections_flag: Print the number of vertices that belong to a face\
             that intersects another face.
+        mask_file: Only compute edge and area stats using vertices in mask.
+        label_file: Only compute edge and area stats using vertices in label.
+        edge_file: Print edge info for all edges into file.
         nogifti_flag: No dump of GIFTI struct, read .gii as surface instead.
         version_flag: Print version and exits.
         help_flag: No clue what this does.
@@ -411,23 +410,23 @@ def mris_info(
         surfacefile=surfacefile,
         outfile=outfile,
         subject_hemi_surfname=subject_hemi_surfname,
+        talairach_xfm_flag=talairach_xfm_flag,
+        rescale_flag=rescale_flag,
         patchfile=patchfile,
         vertex_number=vertex_number,
         extended_vertex_number=extended_vertex_number,
         curvfile=curvfile,
         annotfile=annotfile,
+        area_stats_flag=area_stats_flag,
         edge_stats_id=edge_stats_id,
         edge_number=edge_number,
         vtxno=vtxno,
         matrix_format=matrix_format,
+        quality_stats_flag=quality_stats_flag,
+        intersections_flag=intersections_flag,
         mask_file=mask_file,
         label_file=label_file,
         edge_file=edge_file,
-        talairach_xfm_flag=talairach_xfm_flag,
-        rescale_flag=rescale_flag,
-        area_stats_flag=area_stats_flag,
-        quality_stats_flag=quality_stats_flag,
-        intersections_flag=intersections_flag,
         nogifti_flag=nogifti_flag,
         version_flag=version_flag,
         help_flag=help_flag,

niwrap_freesurfer/freesurfer/mris_label_calc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LABEL_CALC_METADATA = Metadata(
-    id="4566c0b5206cd4d9fc63822cdb713e50b1ee033e.boutiques",
+    id="0dc4043ecf2e55b53be6b5910c84a71bf8a1c707.boutiques",
     name="mris_label_calc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -19,6 +19,7 @@ MrisLabelCalcParameters = typing.TypedDict('MrisLabelCalcParameters', {
     "input1": InputPathType,
     "input2": InputPathType,
     "output": str,
+    "iterations": typing.NotRequired[int | None],
 })
 
 
@@ -69,6 +70,7 @@ def mris_label_calc_params(
     input1: InputPathType,
     input2: InputPathType,
     output: str,
+    iterations: int | None = None,
 ) -> MrisLabelCalcParameters:
     """
     Build parameters.
@@ -79,6 +81,7 @@ def mris_label_calc_params(
         input2: Second input label file (used for 'invert', 'erode', 'dilate'\
             operations).
         output: Output label file.
+        iterations: Number of times to erode or dilate label.
     Returns:
         Parameter dictionary
     """
@@ -89,6 +92,8 @@ def mris_label_calc_params(
         "input2": input2,
         "output": output,
     }
+    if iterations is not None:
+        params["iterations"] = iterations
     return params
 
 
@@ -111,6 +116,11 @@ def mris_label_calc_cargs(
     cargs.append(execution.input_file(params.get("input1")))
     cargs.append(execution.input_file(params.get("input2")))
     cargs.append(params.get("output"))
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "<n>",
+            str(params.get("iterations"))
+        ])
     return cargs
 
 
@@ -163,6 +173,7 @@ def mris_label_calc(
     input1: InputPathType,
     input2: InputPathType,
     output: str,
+    iterations: int | None = None,
     runner: Runner | None = None,
 ) -> MrisLabelCalcOutputs:
     """
@@ -178,6 +189,7 @@ def mris_label_calc(
         input2: Second input label file (used for 'invert', 'erode', 'dilate'\
             operations).
         output: Output label file.
+        iterations: Number of times to erode or dilate label.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLabelCalcOutputs`).
@@ -189,6 +201,7 @@ def mris_label_calc(
         input1=input1,
         input2=input2,
         output=output,
+        iterations=iterations,
     )
     return mris_label_calc_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mris_map_cuts.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MAP_CUTS_METADATA = Metadata(
-    id="779b9e3d194c64fbf7ebe1bfe928f56ccdd44441.boutiques",
+    id="c694d790811be0a427c0f191c8203d1e2914b980.boutiques",
     name="mris_map_cuts",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -95,7 +95,6 @@ def mris_map_cuts_cargs(
     """
     cargs = []
     cargs.append("mris_map_cuts")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_patch")))
     cargs.append(params.get("output_patch"))
     return cargs