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

niwrap_freesurfer/freesurfer/morph_tables_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_TABLES_RH_METADATA = Metadata(
-    id="2f3add04b35d7726ca806ca38014821260043ebc.boutiques",
+    id="9194a1ddf4531bb86d7ff7792d74bb6bd3e661a5.boutiques",
     name="morph_tables-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -91,10 +91,11 @@ def morph_tables_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("morph_tables-rh")
     if params.get("options") is not None:
         cargs.extend([
             "-rh",
-            "morph_tables" + params.get("options")
+            params.get("options")
         ])
     return cargs
 

niwrap_freesurfer/freesurfer/mri_aparc2aseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_APARC2ASEG_METADATA = Metadata(
-    id="70399c00183edd73f6d174d9a1c242615869d650.boutiques",
+    id="d81366f82e290a78f07433462eedcb07c712e3e6.boutiques",
     name="mri_aparc2aseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -31,6 +31,7 @@ MriAparc2asegParameters = typing.TypedDict('MriAparc2asegParameters', {
     "no_fix_parahip": bool,
     "smooth_normals": typing.NotRequired[float | None],
     "crs_test": typing.NotRequired[str | None],
+    "left_hemisphere": bool,
     "right_hemisphere": bool,
     "threads": typing.NotRequired[float | None],
     "help": bool,
@@ -97,6 +98,7 @@ def mri_aparc2aseg_params(
     no_fix_parahip: bool = False,
     smooth_normals: float | None = None,
     crs_test: str | None = None,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     threads: float | None = None,
     help_: bool = False,
@@ -130,6 +132,7 @@ def mri_aparc2aseg_params(
         smooth_normals: Change number of surface normal smoothing steps\
             (default is 10).
         crs_test: Test mapping of column, row, slice.
+        left_hemisphere: Only process the left hemisphere.
         right_hemisphere: Only process the right hemisphere.
         threads: Run in parallel with the specified number of threads.
         help_: Print out information on how to use this program.
@@ -147,6 +150,7 @@ def mri_aparc2aseg_params(
         "rip_unknown": rip_unknown,
         "hypo_as_wm": hypo_as_wm,
         "no_fix_parahip": no_fix_parahip,
+        "left_hemisphere": left_hemisphere,
         "right_hemisphere": right_hemisphere,
         "help": help_,
         "version": version,
@@ -243,6 +247,8 @@ def mri_aparc2aseg_cargs(
             "--crs-test",
             params.get("crs_test")
         ])
+    if params.get("left_hemisphere"):
+        cargs.append("--lh")
     if params.get("right_hemisphere"):
         cargs.append("--rh")
     if params.get("threads") is not None:
@@ -319,6 +325,7 @@ def mri_aparc2aseg(
     no_fix_parahip: bool = False,
     smooth_normals: float | None = None,
     crs_test: str | None = None,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     threads: float | None = None,
     help_: bool = False,
@@ -358,6 +365,7 @@ def mri_aparc2aseg(
         smooth_normals: Change number of surface normal smoothing steps\
             (default is 10).
         crs_test: Test mapping of column, row, slice.
+        left_hemisphere: Only process the left hemisphere.
         right_hemisphere: Only process the right hemisphere.
         threads: Run in parallel with the specified number of threads.
         help_: Print out information on how to use this program.
@@ -385,6 +393,7 @@ def mri_aparc2aseg(
         no_fix_parahip=no_fix_parahip,
         smooth_normals=smooth_normals,
         crs_test=crs_test,
+        left_hemisphere=left_hemisphere,
         right_hemisphere=right_hemisphere,
         threads=threads,
         help_=help_,

niwrap_freesurfer/freesurfer/mri_apply_bias.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_APPLY_BIAS_METADATA = Metadata(
-    id="b81c79a708e537c2c711365f270f39010a6db69c.boutiques",
+    id="8cf82e2100484415318613b93b2e614090b1cce0.boutiques",
     name="mri_apply_bias",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -102,7 +102,6 @@ def mri_apply_bias_cargs(
     """
     cargs = []
     cargs.append("mri_apply_bias")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_volume")))
     cargs.append(execution.input_file(params.get("bias_volume")))
     cargs.append(params.get("output_volume"))

niwrap_freesurfer/freesurfer/mri_average.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_AVERAGE_METADATA = Metadata(
-    id="9f634edc8e7e1a23500b288fecc20c4dd605a410.boutiques",
+    id="69d82dea302095f344b973c4241c98b9f485dab8.boutiques",
     name="mri_average",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -31,6 +31,7 @@ MriAverageParameters = typing.TypedDict('MriAverageParameters', {
     "translation": typing.NotRequired[list[float] | None],
     "rotation": typing.NotRequired[list[float] | None],
     "momentum": typing.NotRequired[float | None],
+    "rms": bool,
     "rms_alt": bool,
     "percent": bool,
     "binarize": typing.NotRequired[float | None],
@@ -97,6 +98,7 @@ def mri_average_params(
     translation: list[float] | None = None,
     rotation: list[float] | None = None,
     momentum: float | None = None,
+    rms: bool = False,
     rms_alt: bool = False,
     percent: bool = False,
     binarize: float | None = None,
@@ -124,6 +126,7 @@ def mri_average_params(
         translation: Translation of second volume.
         rotation: Rotation of second volume around each axis in degrees.
         momentum: Use momentum n (default=0).
+        rms: Compute sqrt of average of sum of squares (RMS, same as -rms).
         rms_alt: Compute sqrt of average of sum of squares (RMS, same as -sqr).
         percent: Compute percentage.
         binarize: Binarize the input volumes using threshold th.
@@ -141,6 +144,7 @@ def mri_average_params(
         "noconform": noconform,
         "trilinear": trilinear,
         "window": window,
+        "rms": rms,
         "rms_alt": rms_alt,
         "percent": percent,
         "absolute": absolute,
@@ -235,6 +239,8 @@ def mri_average_cargs(
             "-m",
             str(params.get("momentum"))
         ])
+    if params.get("rms"):
+        cargs.append("-sqr")
     if params.get("rms_alt"):
         cargs.append("-rms")
     if params.get("percent"):
@@ -311,6 +317,7 @@ def mri_average(
     translation: list[float] | None = None,
     rotation: list[float] | None = None,
     momentum: float | None = None,
+    rms: bool = False,
     rms_alt: bool = False,
     percent: bool = False,
     binarize: float | None = None,
@@ -344,6 +351,7 @@ def mri_average(
         translation: Translation of second volume.
         rotation: Rotation of second volume around each axis in degrees.
         momentum: Use momentum n (default=0).
+        rms: Compute sqrt of average of sum of squares (RMS, same as -rms).
         rms_alt: Compute sqrt of average of sum of squares (RMS, same as -sqr).
         percent: Compute percentage.
         binarize: Binarize the input volumes using threshold th.
@@ -371,6 +379,7 @@ def mri_average(
         translation=translation,
         rotation=rotation,
         momentum=momentum,
+        rms=rms,
         rms_alt=rms_alt,
         percent=percent,
         binarize=binarize,

niwrap_freesurfer/freesurfer/mri_brain_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_BRAIN_VOLUME_METADATA = Metadata(
-    id="7e192aa897893490560e7414f5f2c974f66d8c71.boutiques",
+    id="7e9a6415798579853848210ef705f99e9ccb5ca0.boutiques",
     name="mri_brain_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,8 @@ MriBrainVolumeParameters = typing.TypedDict('MriBrainVolumeParameters', {
     "__STYX_TYPE__": typing.Literal["mri_brain_volume"],
     "input_file": InputPathType,
     "output_file": typing.NotRequired[str | None],
+    "force_param": typing.NotRequired[float | None],
+    "version": bool,
 })
 
 
@@ -65,6 +67,8 @@ class MriBrainVolumeOutputs(typing.NamedTuple):
 def mri_brain_volume_params(
     input_file: InputPathType,
     output_file: str | None = None,
+    force_param: float | None = None,
+    version: bool = False,
 ) -> MriBrainVolumeParameters:
     """
     Build parameters.
@@ -72,15 +76,20 @@ def mri_brain_volume_params(
     Args:
         input_file: Input MRI file.
         output_file: Output file for brain volume.
+        force_param: Change pushout force (default 1.0).
+        version: Show the current version.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "mri_brain_volume",
         "input_file": input_file,
+        "version": version,
     }
     if output_file is not None:
         params["output_file"] = output_file
+    if force_param is not None:
+        params["force_param"] = force_param
     return params
 
 
@@ -99,10 +108,16 @@ def mri_brain_volume_cargs(
     """
     cargs = []
     cargs.append("mri_brain_volume")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("input_file")))
     if params.get("output_file") is not None:
         cargs.append(params.get("output_file"))
+    if params.get("force_param") is not None:
+        cargs.extend([
+            "-forceParam",
+            str(params.get("force_param"))
+        ])
+    if params.get("version"):
+        cargs.append("--version")
     return cargs
 
 
@@ -153,6 +168,8 @@ def mri_brain_volume_execute(
 def mri_brain_volume(
     input_file: InputPathType,
     output_file: str | None = None,
+    force_param: float | None = None,
+    version: bool = False,
     runner: Runner | None = None,
 ) -> MriBrainVolumeOutputs:
     """
@@ -165,6 +182,8 @@ def mri_brain_volume(
     Args:
         input_file: Input MRI file.
         output_file: Output file for brain volume.
+        force_param: Change pushout force (default 1.0).
+        version: Show the current version.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriBrainVolumeOutputs`).
@@ -174,6 +193,8 @@ def mri_brain_volume(
     params = mri_brain_volume_params(
         input_file=input_file,
         output_file=output_file,
+        force_param=force_param,
+        version=version,
     )
     return mri_brain_volume_execute(params, execution)