niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/aseg2feat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ASEG2FEAT_METADATA = Metadata(
-    id="b7b7dd7d021ba889f028fd69296eae3f1560ec42.boutiques",
+    id="2011d2b6f3028266f6fb20403a720745aaeb17d4.boutiques",
     name="aseg2feat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ ASEG2FEAT_METADATA = Metadata(
 
 
 Aseg2featParameters = typing.TypedDict('Aseg2featParameters', {
-    "__STYXTYPE__": typing.Literal["aseg2feat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/aseg2feat"]],
+    "feat": str,
+    "featdirfile": typing.NotRequired[InputPathType | None],
+    "seg": typing.NotRequired[str | None],
+    "aparc_aseg": bool,
+    "svstats": bool,
+    "standard": bool,
+    "debug": bool,
+    "help": bool,
+    "version": bool,
+})
+Aseg2featParametersTagged = typing.TypedDict('Aseg2featParametersTagged', {
+    "@type": typing.Literal["freesurfer/aseg2feat"],
     "feat": str,
     "featdirfile": typing.NotRequired[InputPathType | None],
     "seg": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ Aseg2featParameters = typing.TypedDict('Aseg2featParameters', {
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "aseg2feat": aseg2feat_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "aseg2feat": aseg2feat_outputs,
-    }.get(t)
 
 
 class Aseg2featOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `aseg2feat(...)`.
+    Output object returned when calling `Aseg2featParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def aseg2feat_params(
     debug: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> Aseg2featParameters:
+) -> Aseg2featParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def aseg2feat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "aseg2feat",
+        "@type": "freesurfer/aseg2feat",
         "feat": feat,
         "aparc_aseg": aparc_aseg,
         "svstats": svstats,
@@ -134,29 +114,29 @@ def aseg2feat_cargs(
     cargs.append("aseg2feat")
     cargs.extend([
         "--feat",
-        params.get("feat")
+        params.get("feat", None)
     ])
-    if params.get("featdirfile") is not None:
+    if params.get("featdirfile", None) is not None:
         cargs.extend([
             "--featdirfile",
-            execution.input_file(params.get("featdirfile"))
+            execution.input_file(params.get("featdirfile", None))
         ])
-    if params.get("seg") is not None:
+    if params.get("seg", None) is not None:
         cargs.extend([
             "--seg",
-            params.get("seg")
+            params.get("seg", None)
         ])
-    if params.get("aparc_aseg"):
+    if params.get("aparc_aseg", False):
         cargs.append("--aparc+aseg")
-    if params.get("svstats"):
+    if params.get("svstats", False):
         cargs.append("--svstats")
-    if params.get("standard"):
+    if params.get("standard", False):
         cargs.append("--standard")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -176,19 +156,21 @@ def aseg2feat_outputs(
     """
     ret = Aseg2featOutputs(
         root=execution.output_file("."),
-        segmentation_output=execution.output_file(params.get("feat") + "/reg/freesurfer/aseg.nii.gz"),
-        stats_output=execution.output_file(params.get("feat") + "/stats"),
+        segmentation_output=execution.output_file(params.get("feat", None) + "/reg/freesurfer/aseg.nii.gz"),
+        stats_output=execution.output_file(params.get("feat", None) + "/stats"),
     )
     return ret
 
 
 def aseg2feat_execute(
     params: Aseg2featParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Aseg2featOutputs:
     """
-    Resamples the FreeSurfer automatic subcortical segmentation (aseg) to the FEAT
-    functional space.
+    aseg2feat
+    
+    Resamples the FreeSurfer automatic subcortical segmentation (aseg) to the
+    FEAT functional space.
     
     Author: FreeSurfer Developers
     
@@ -196,10 +178,12 @@ def aseg2feat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Aseg2featOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ASEG2FEAT_METADATA)
     params = execution.params(params)
     cargs = aseg2feat_cargs(params, execution)
     ret = aseg2feat_outputs(params, execution)
@@ -220,8 +204,10 @@ def aseg2feat(
     runner: Runner | None = None,
 ) -> Aseg2featOutputs:
     """
-    Resamples the FreeSurfer automatic subcortical segmentation (aseg) to the FEAT
-    functional space.
+    aseg2feat
+    
+    Resamples the FreeSurfer automatic subcortical segmentation (aseg) to the
+    FEAT functional space.
     
     Author: FreeSurfer Developers
     
@@ -243,8 +229,6 @@ def aseg2feat(
     Returns:
         NamedTuple of outputs (described in `Aseg2featOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ASEG2FEAT_METADATA)
     params = aseg2feat_params(
         feat=feat,
         featdirfile=featdirfile,
@@ -256,13 +240,13 @@ def aseg2feat(
         help_=help_,
         version=version,
     )
-    return aseg2feat_execute(params, execution)
+    return aseg2feat_execute(params, runner)
 
 
 __all__ = [
     "ASEG2FEAT_METADATA",
     "Aseg2featOutputs",
-    "Aseg2featParameters",
     "aseg2feat",
+    "aseg2feat_execute",
     "aseg2feat_params",
 ]

niwrap_freesurfer/freesurfer/asegstats2table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ASEGSTATS2TABLE_METADATA = Metadata(
-    id="913ffe3689796073b891a61e20a937aa44732063.boutiques",
+    id="72305d9ab5ffacd0859b26cb93dda15aaa6787ac.boutiques",
     name="asegstats2table",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,34 @@ ASEGSTATS2TABLE_METADATA = Metadata(
 
 
 Asegstats2tableParameters = typing.TypedDict('Asegstats2tableParameters', {
-    "__STYXTYPE__": typing.Literal["asegstats2table"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/asegstats2table"]],
+    "subjects": typing.NotRequired[list[str] | None],
+    "inputs": typing.NotRequired[list[str] | None],
+    "tablefile": str,
+    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "qdec": typing.NotRequired[InputPathType | None],
+    "qdec_long": typing.NotRequired[InputPathType | None],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "maxsegno": typing.NotRequired[list[str] | None],
+    "segids_from_file": typing.NotRequired[InputPathType | None],
+    "segno_include": typing.NotRequired[list[str] | None],
+    "segno_exclude": typing.NotRequired[list[str] | None],
+    "measure": typing.NotRequired[str | None],
+    "delimiter": typing.NotRequired[str | None],
+    "statsfile": typing.NotRequired[str | None],
+    "subdir": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "write_etiv": bool,
+    "debug": bool,
+    "transpose_flag": bool,
+    "common_segs_flag": bool,
+    "all_segs_flag": bool,
+    "no_vol_extras_flag": bool,
+    "skip_missing_flag": bool,
+    "replace53_flag": bool,
+})
+Asegstats2tableParametersTagged = typing.TypedDict('Asegstats2tableParametersTagged', {
+    "@type": typing.Literal["freesurfer/asegstats2table"],
     "subjects": typing.NotRequired[list[str] | None],
     "inputs": typing.NotRequired[list[str] | None],
     "tablefile": str,
@@ -40,43 +67,11 @@ Asegstats2tableParameters = typing.TypedDict('Asegstats2tableParameters', {
     "skip_missing_flag": bool,
     "replace53_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "asegstats2table": asegstats2table_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "asegstats2table": asegstats2table_outputs,
-    }.get(t)
 
 
 class Asegstats2tableOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `asegstats2table(...)`.
+    Output object returned when calling `Asegstats2tableParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -109,7 +104,7 @@ def asegstats2table_params(
     no_vol_extras_flag: bool = False,
     skip_missing_flag: bool = False,
     replace53_flag: bool = False,
-) -> Asegstats2tableParameters:
+) -> Asegstats2tableParametersTagged:
     """
     Build parameters.
     
@@ -152,7 +147,7 @@ def asegstats2table_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "asegstats2table",
+        "@type": "freesurfer/asegstats2table",
         "tablefile": tablefile,
         "write_etiv": write_etiv,
         "debug": debug,
@@ -211,100 +206,100 @@ def asegstats2table_cargs(
     """
     cargs = []
     cargs.append("asegstats2table")
-    if params.get("subjects") is not None:
+    if params.get("subjects", None) is not None:
         cargs.extend([
             "--subjects",
-            *params.get("subjects")
+            *params.get("subjects", None)
         ])
-    if params.get("inputs") is not None:
+    if params.get("inputs", None) is not None:
         cargs.extend([
             "--inputs",
-            *params.get("inputs")
+            *params.get("inputs", None)
         ])
     cargs.extend([
         "--tablefile",
-        params.get("tablefile")
+        params.get("tablefile", None)
     ])
-    if params.get("subjectsfile") is not None:
+    if params.get("subjectsfile", None) is not None:
         cargs.extend([
             "--subjectsfile",
-            execution.input_file(params.get("subjectsfile"))
+            execution.input_file(params.get("subjectsfile", None))
         ])
-    if params.get("qdec") is not None:
+    if params.get("qdec", None) is not None:
         cargs.extend([
             "--qdec",
-            execution.input_file(params.get("qdec"))
+            execution.input_file(params.get("qdec", None))
         ])
-    if params.get("qdec_long") is not None:
+    if params.get("qdec_long", None) is not None:
         cargs.extend([
             "--qdec-long",
-            execution.input_file(params.get("qdec_long"))
+            execution.input_file(params.get("qdec_long", None))
         ])
-    if params.get("fsgd") is not None:
+    if params.get("fsgd", None) is not None:
         cargs.extend([
             "--fsgd",
-            execution.input_file(params.get("fsgd"))
+            execution.input_file(params.get("fsgd", None))
         ])
-    if params.get("maxsegno") is not None:
+    if params.get("maxsegno", None) is not None:
         cargs.extend([
             "--maxsegno",
-            *params.get("maxsegno")
+            *params.get("maxsegno", None)
         ])
-    if params.get("segids_from_file") is not None:
+    if params.get("segids_from_file", None) is not None:
         cargs.extend([
             "--segids-from-file",
-            execution.input_file(params.get("segids_from_file"))
+            execution.input_file(params.get("segids_from_file", None))
         ])
-    if params.get("segno_include") is not None:
+    if params.get("segno_include", None) is not None:
         cargs.extend([
             "--segno",
-            *params.get("segno_include")
+            *params.get("segno_include", None)
         ])
-    if params.get("segno_exclude") is not None:
+    if params.get("segno_exclude", None) is not None:
         cargs.extend([
             "--no-segno",
-            *params.get("segno_exclude")
+            *params.get("segno_exclude", None)
         ])
-    if params.get("measure") is not None:
+    if params.get("measure", None) is not None:
         cargs.extend([
             "--meas",
-            params.get("measure")
+            params.get("measure", None)
         ])
-    if params.get("delimiter") is not None:
+    if params.get("delimiter", None) is not None:
         cargs.extend([
             "--delimiter",
-            params.get("delimiter")
+            params.get("delimiter", None)
         ])
-    if params.get("statsfile") is not None:
+    if params.get("statsfile", None) is not None:
         cargs.extend([
             "--statsfile",
-            params.get("statsfile")
+            params.get("statsfile", None)
         ])
-    if params.get("subdir") is not None:
+    if params.get("subdir", None) is not None:
         cargs.extend([
             "--subdir",
-            params.get("subdir")
+            params.get("subdir", None)
         ])
-    if params.get("scale") is not None:
+    if params.get("scale", None) is not None:
         cargs.extend([
             "--scale",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
-    if params.get("write_etiv"):
+    if params.get("write_etiv", False):
         cargs.append("--etiv")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("transpose_flag"):
+    if params.get("transpose_flag", False):
         cargs.append("--transpose")
-    if params.get("common_segs_flag"):
+    if params.get("common_segs_flag", False):
         cargs.append("--common-segs")
-    if params.get("all_segs_flag"):
+    if params.get("all_segs_flag", False):
         cargs.append("--all-segs")
-    if params.get("no_vol_extras_flag"):
+    if params.get("no_vol_extras_flag", False):
         cargs.append("--no-vol-extras")
-    if params.get("skip_missing_flag"):
+    if params.get("skip_missing_flag", False):
         cargs.append("--skip")
-    if params.get("replace53_flag"):
+    if params.get("replace53_flag", False):
         cargs.append("--replace53")
     return cargs
 
@@ -324,16 +319,18 @@ def asegstats2table_outputs(
     """
     ret = Asegstats2tableOutputs(
         root=execution.output_file("."),
-        output_table=execution.output_file(params.get("tablefile")),
+        output_table=execution.output_file(params.get("tablefile", None)),
     )
     return ret
 
 
 def asegstats2table_execute(
     params: Asegstats2tableParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Asegstats2tableOutputs:
     """
+    asegstats2table
+    
     Converts a subcortical stats file created by recon-all and/or mri_segstats
     (e.g., aseg.stats) into a table.
     
@@ -343,10 +340,12 @@ def asegstats2table_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Asegstats2tableOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ASEGSTATS2TABLE_METADATA)
     params = execution.params(params)
     cargs = asegstats2table_cargs(params, execution)
     ret = asegstats2table_outputs(params, execution)
@@ -382,6 +381,8 @@ def asegstats2table(
     runner: Runner | None = None,
 ) -> Asegstats2tableOutputs:
     """
+    asegstats2table
+    
     Converts a subcortical stats file created by recon-all and/or mri_segstats
     (e.g., aseg.stats) into a table.
     
@@ -428,8 +429,6 @@ def asegstats2table(
     Returns:
         NamedTuple of outputs (described in `Asegstats2tableOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ASEGSTATS2TABLE_METADATA)
     params = asegstats2table_params(
         subjects=subjects,
         inputs=inputs,
@@ -456,13 +455,13 @@ def asegstats2table(
         skip_missing_flag=skip_missing_flag,
         replace53_flag=replace53_flag,
     )
-    return asegstats2table_execute(params, execution)
+    return asegstats2table_execute(params, runner)
 
 
 __all__ = [
     "ASEGSTATS2TABLE_METADATA",
     "Asegstats2tableOutputs",
-    "Asegstats2tableParameters",
     "asegstats2table",
+    "asegstats2table_execute",
     "asegstats2table_params",
 ]

niwrap_freesurfer/freesurfer/asegstatsdiff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ASEGSTATSDIFF_METADATA = Metadata(
-    id="db6a58e5c841a394a7bf194df11a9bf8523b88c1.boutiques",
+    id="9b4e27fd2feda16f3e1e17a8f4d265fba2c077ae.boutiques",
     name="asegstatsdiff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ ASEGSTATSDIFF_METADATA = Metadata(
 
 
 AsegstatsdiffParameters = typing.TypedDict('AsegstatsdiffParameters', {
-    "__STYXTYPE__": typing.Literal["asegstatsdiff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/asegstatsdiff"]],
+    "subject1": str,
+    "subject2": str,
+    "outdir": typing.NotRequired[str | None],
+})
+AsegstatsdiffParametersTagged = typing.TypedDict('AsegstatsdiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/asegstatsdiff"],
     "subject1": str,
     "subject2": str,
     "outdir": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "asegstatsdiff": asegstatsdiff_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "asegstatsdiff": asegstatsdiff_outputs,
-    }.get(t)
 
 
 class AsegstatsdiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `asegstatsdiff(...)`.
+    Output object returned when calling `AsegstatsdiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def asegstatsdiff_params(
     subject1: str,
     subject2: str,
     outdir: str | None = None,
-) -> AsegstatsdiffParameters:
+) -> AsegstatsdiffParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def asegstatsdiff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "asegstatsdiff",
+        "@type": "freesurfer/asegstatsdiff",
         "subject1": subject1,
         "subject2": subject2,
     }
@@ -104,9 +78,9 @@ def asegstatsdiff_cargs(
     """
     cargs = []
     cargs.append("asegstatsdiff")
-    cargs.append(params.get("subject1"))
-    if params.get("outdir") is not None:
-        cargs.append(params.get("subject2") + params.get("outdir"))
+    cargs.append(params.get("subject1", None))
+    if params.get("outdir", None) is not None:
+        cargs.append(params.get("subject2", None) + params.get("outdir", None))
     return cargs
 
 
@@ -125,18 +99,20 @@ def asegstatsdiff_outputs(
     """
     ret = AsegstatsdiffOutputs(
         root=execution.output_file("."),
-        asegstats_output=execution.output_file(params.get("outdir") + "/asegstats.txt") if (params.get("outdir") is not None) else None,
+        asegstats_output=execution.output_file(params.get("outdir", None) + "/asegstats.txt") if (params.get("outdir") is not None) else None,
     )
     return ret
 
 
 def asegstatsdiff_execute(
     params: AsegstatsdiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AsegstatsdiffOutputs:
     """
-    Compute and report percentage differences in aseg morphometry data between two
-    subjects.
+    asegstatsdiff
+    
+    Compute and report percentage differences in aseg morphometry data between
+    two subjects.
     
     Author: FreeSurfer Developers
     
@@ -144,10 +120,12 @@ def asegstatsdiff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AsegstatsdiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ASEGSTATSDIFF_METADATA)
     params = execution.params(params)
     cargs = asegstatsdiff_cargs(params, execution)
     ret = asegstatsdiff_outputs(params, execution)
@@ -162,8 +140,10 @@ def asegstatsdiff(
     runner: Runner | None = None,
 ) -> AsegstatsdiffOutputs:
     """
-    Compute and report percentage differences in aseg morphometry data between two
-    subjects.
+    asegstatsdiff
+    
+    Compute and report percentage differences in aseg morphometry data between
+    two subjects.
     
     Author: FreeSurfer Developers
     
@@ -178,20 +158,18 @@ def asegstatsdiff(
     Returns:
         NamedTuple of outputs (described in `AsegstatsdiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ASEGSTATSDIFF_METADATA)
     params = asegstatsdiff_params(
         subject1=subject1,
         subject2=subject2,
         outdir=outdir,
     )
-    return asegstatsdiff_execute(params, execution)
+    return asegstatsdiff_execute(params, runner)
 
 
 __all__ = [
     "ASEGSTATSDIFF_METADATA",
     "AsegstatsdiffOutputs",
-    "AsegstatsdiffParameters",
     "asegstatsdiff",
+    "asegstatsdiff_execute",
     "asegstatsdiff_params",
 ]