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

niwrap_freesurfer/freesurfer/run_qdec_glm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_QDEC_GLM_METADATA = Metadata(
-    id="b83d7c50b5137b0f5530f2c1776edefd9de98fa2.boutiques",
+    id="7d86461bf7f65d864302de80bed43c2de8adbb76.boutiques",
     name="run-qdec-glm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def run_qdec_glm_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("run-qdec-glm")
     cargs.extend([
         "-glm",
-        "run-qdec" + params.get("qdec_directory")
+        params.get("qdec_directory")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/samseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMSEG_METADATA = Metadata(
-    id="1947f646fba1c79e354f5efabbda10d0a11595ce.boutiques",
+    id="86da9ab5c96ce79b11eaa8ba3fee321e3bcca1b7.boutiques",
     name="samseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -52,6 +52,7 @@ SamsegParameters = typing.TypedDict('SamsegParameters', {
     "regmat_file": typing.NotRequired[InputPathType | None],
     "init_lta": typing.NotRequired[InputPathType | None],
     "reg_only": bool,
+    "ssdd_directory": typing.NotRequired[str | None],
     "save_mesh": bool,
     "max_iters": typing.NotRequired[float | None],
     "dice_file": typing.NotRequired[InputPathType | None],
@@ -147,6 +148,7 @@ def samseg_params(
     regmat_file: InputPathType | None = None,
     init_lta: InputPathType | None = None,
     reg_only: bool = False,
+    ssdd_directory: str | None = None,
     save_mesh: bool = False,
     max_iters: float | None = None,
     dice_file: InputPathType | None = None,
@@ -207,6 +209,7 @@ def samseg_params(
         regmat_file: Same as --reg.
         init_lta: Initial registration LTA file.
         reg_only: Only perform registration.
+        ssdd_directory: Path to SAMSEG_Data_DIR where the atlas is located.
         save_mesh: Save the mesh, useful for longitudinal analysis.
         max_iters: Maximum number of iterations.
         dice_file: DICE coefficient file for segmentation.
@@ -277,6 +280,8 @@ def samseg_params(
         params["regmat_file"] = regmat_file
     if init_lta is not None:
         params["init_lta"] = init_lta
+    if ssdd_directory is not None:
+        params["ssdd_directory"] = ssdd_directory
     if max_iters is not None:
         params["max_iters"] = max_iters
     if dice_file is not None:
@@ -432,6 +437,11 @@ def samseg_cargs(
         ])
     if params.get("reg_only"):
         cargs.append("--reg-only")
+    if params.get("ssdd_directory") is not None:
+        cargs.extend([
+            "--ssdd",
+            params.get("ssdd_directory")
+        ])
     if params.get("save_mesh"):
         cargs.append("--save-mesh")
     if params.get("max_iters") is not None:
@@ -545,6 +555,7 @@ def samseg(
     regmat_file: InputPathType | None = None,
     init_lta: InputPathType | None = None,
     reg_only: bool = False,
+    ssdd_directory: str | None = None,
     save_mesh: bool = False,
     max_iters: float | None = None,
     dice_file: InputPathType | None = None,
@@ -611,6 +622,7 @@ def samseg(
         regmat_file: Same as --reg.
         init_lta: Initial registration LTA file.
         reg_only: Only perform registration.
+        ssdd_directory: Path to SAMSEG_Data_DIR where the atlas is located.
         save_mesh: Save the mesh, useful for longitudinal analysis.
         max_iters: Maximum number of iterations.
         dice_file: DICE coefficient file for segmentation.
@@ -663,6 +675,7 @@ def samseg(
         regmat_file=regmat_file,
         init_lta=init_lta,
         reg_only=reg_only,
+        ssdd_directory=ssdd_directory,
         save_mesh=save_mesh,
         max_iters=max_iters,
         dice_file=dice_file,

niwrap_freesurfer/freesurfer/samseg_long.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMSEG_LONG_METADATA = Metadata(
-    id="686e2f45cf8bcf8f37552255f101cc1d16f93f40.boutiques",
+    id="514c1dbb1911d4434a75fb9f1d1ec8a2a10ee435.boutiques",
     name="samseg-long",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,9 +16,10 @@ SAMSEG_LONG_METADATA = Metadata(
 SamsegLongParameters = typing.TypedDict('SamsegLongParameters', {
     "__STYX_TYPE__": typing.Literal["samseg-long"],
     "output_dir": str,
+    "input_files": list[InputPathType],
+    "align_mc": bool,
     "align_no_mc": bool,
     "threads": typing.NotRequired[float | None],
-    "input_files": list[InputPathType],
     "save_posteriors": bool,
     "force_update": bool,
 })
@@ -73,6 +74,7 @@ class SamsegLongOutputs(typing.NamedTuple):
 def samseg_long_params(
     output_dir: str,
     input_files: list[InputPathType],
+    align_mc: bool = False,
     align_no_mc: bool = False,
     threads: float | None = None,
     save_posteriors: bool = False,
@@ -84,6 +86,7 @@ def samseg_long_params(
     Args:
         output_dir: Output directory.
         input_files: Input image files. All inputs must be a single modality.
+        align_mc: Align all inputs using robust register.
         align_no_mc: Do not align inputs using robust register.
         threads: Number of threads to use.
         save_posteriors: Save posterior probabilities.
@@ -94,8 +97,9 @@ def samseg_long_params(
     params = {
         "__STYXTYPE__": "samseg-long",
         "output_dir": output_dir,
-        "align_no_mc": align_no_mc,
         "input_files": input_files,
+        "align_mc": align_mc,
+        "align_no_mc": align_no_mc,
         "save_posteriors": save_posteriors,
         "force_update": force_update,
     }
@@ -123,6 +127,12 @@ def samseg_long_cargs(
         "--o",
         params.get("output_dir")
     ])
+    cargs.extend([
+        "--i",
+        *[execution.input_file(f) for f in params.get("input_files")]
+    ])
+    if params.get("align_mc"):
+        cargs.append("--mc")
     if params.get("align_no_mc"):
         cargs.append("--no-mc")
     if params.get("threads") is not None:
@@ -130,10 +140,6 @@ def samseg_long_cargs(
             "--threads",
             str(params.get("threads"))
         ])
-    cargs.extend([
-        "--i",
-        *[execution.input_file(f) for f in params.get("input_files")]
-    ])
     if params.get("save_posteriors"):
         cargs.append("--save-posteriors")
     if params.get("force_update"):
@@ -190,6 +196,7 @@ def samseg_long_execute(
 def samseg_long(
     output_dir: str,
     input_files: list[InputPathType],
+    align_mc: bool = False,
     align_no_mc: bool = False,
     threads: float | None = None,
     save_posteriors: bool = False,
@@ -206,6 +213,7 @@ def samseg_long(
     Args:
         output_dir: Output directory.
         input_files: Input image files. All inputs must be a single modality.
+        align_mc: Align all inputs using robust register.
         align_no_mc: Do not align inputs using robust register.
         threads: Number of threads to use.
         save_posteriors: Save posterior probabilities.
@@ -218,9 +226,10 @@ def samseg_long(
     execution = runner.start_execution(SAMSEG_LONG_METADATA)
     params = samseg_long_params(
         output_dir=output_dir,
+        input_files=input_files,
+        align_mc=align_mc,
         align_no_mc=align_no_mc,
         threads=threads,
-        input_files=input_files,
         save_posteriors=save_posteriors,
         force_update=force_update,
     )

niwrap_freesurfer/freesurfer/samsegmesh2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMSEGMESH2SURF_METADATA = Metadata(
-    id="d985be1373714eb0aff1a308730598604fe9d68c.boutiques",
+    id="d0ca6a468bc9a3a09b97395c0b760ba787b54209.boutiques",
     name="samsegmesh2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -127,24 +127,22 @@ def samsegmesh2surf_cargs(
     if params.get("template") is not None:
         cargs.extend([
             "--template",
-            "(" + execution.input_file(params.get("template"))
+            execution.input_file(params.get("template"))
         ])
-    cargs.append("|")
     if params.get("lta_transform") is not None:
         cargs.extend([
             "--lta",
-            execution.input_file(params.get("lta_transform")) + ")"
+            execution.input_file(params.get("lta_transform"))
         ])
     if params.get("output_surface") is not None:
         cargs.extend([
             "--osurf",
-            "(" + params.get("output_surface")
+            params.get("output_surface")
         ])
-    cargs.append("|")
     if params.get("output_priors") is not None:
         cargs.extend([
             "--opriors",
-            params.get("output_priors") + ")"
+            params.get("output_priors")
         ])
     if params.get("invert_flag"):
         cargs.append("--invert")

niwrap_freesurfer/freesurfer/seg2filled.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEG2FILLED_METADATA = Metadata(
-    id="894fcea3b0a2a4a1b34ad187f3a8016973d50857.boutiques",
+    id="08a923890854a31a1c2fa48662a53980de38b6b2.boutiques",
     name="seg2filled",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -123,15 +123,15 @@ def seg2filled_cargs(
     cargs.append("seg2filled")
     cargs.extend([
         "-seg",
-        "-" + execution.input_file(params.get("seg_file"))
+        execution.input_file(params.get("seg_file"))
     ])
     cargs.extend([
         "-norm",
-        "-" + execution.input_file(params.get("norm_file"))
+        execution.input_file(params.get("norm_file"))
     ])
     cargs.extend([
         "-o",
-        "-" + params.get("output_file")
+        params.get("output_file")
     ])
     if params.get("ndil") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/segment_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_METADATA = Metadata(
-    id="5ab5fa41476c4d8921b2a5ed52d0505305a8ad2b.boutiques",
+    id="a65e75f6b6b5d6e1393a6f72d663a2e7389bbdf7.boutiques",
     name="segment_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -114,7 +114,7 @@ def segment_subject_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_nu_correct.mni")
+    cargs.append("segment_subject")
     cargs.extend([
         "--i",
         execution.input_file(params.get("input_volume"))

niwrap_freesurfer/freesurfer/segment_subject_old_skull_strip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA = Metadata(
-    id="abc48359fac304f034867897b978186bcd82c5e7.boutiques",
+    id="76e6c0d1bcca0bcd9cea638d24de4bcebaf7875a.boutiques",
     name="segment_subject_old_skull_strip",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -116,14 +116,14 @@ def segment_subject_old_skull_strip_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_nu_correct.mni")
+    cargs.append("segment_subject_old_skull_strip")
     cargs.extend([
         "-i",
-        "-" + execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume"))
     ])
     cargs.extend([
         "-xfm",
-        "-" + params.get("output_xfm")
+        params.get("output_xfm")
     ])
     if params.get("log_file") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/segment_subject_sc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_SC_METADATA = Metadata(
-    id="02733a36fda91e4ab91ac726bedcbf25c9c93313.boutiques",
+    id="fa16d65c7df23bac2f3fce0055543daf1ef20f51.boutiques",
     name="segment_subject_sc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -106,14 +106,14 @@ def segment_subject_sc_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_nu_correct.mni")
+    cargs.append("segment_subject_sc")
     cargs.extend([
         "-i",
-        "-" + execution.input_file(params.get("invol"))
+        execution.input_file(params.get("invol"))
     ])
     cargs.extend([
         "-xfm",
-        "-" + execution.input_file(params.get("outxfm"))
+        execution.input_file(params.get("outxfm"))
     ])
     if params.get("log") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/segment_subject_t2_auto_estimate_alveus_ml.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
-    id="8a6a12eb1eae4567d49625f69155e84f68466b3c.boutiques",
+    id="e6b692a7de46610579fa5e10ad01fb96c5b2f745.boutiques",
     name="segmentSubjectT2_autoEstimateAlveusML",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,7 @@ SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
 
 SegmentSubjectT2AutoEstimateAlveusMlParameters = typing.TypedDict('SegmentSubjectT2AutoEstimateAlveusMlParameters', {
     "__STYX_TYPE__": typing.Literal["segmentSubjectT2_autoEstimateAlveusML"],
+    "missing_library": str,
 })
 
 
@@ -58,16 +59,20 @@ class SegmentSubjectT2AutoEstimateAlveusMlOutputs(typing.NamedTuple):
 
 
 def segment_subject_t2_auto_estimate_alveus_ml_params(
+    missing_library: str = "libmwlaunchermain.so: cannot open shared object file",
 ) -> SegmentSubjectT2AutoEstimateAlveusMlParameters:
     """
     Build parameters.
     
     Args:
+        missing_library: The tool could not be executed due to a missing shared\
+            library: libmwlaunchermain.so.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "segmentSubjectT2_autoEstimateAlveusML",
+        "missing_library": missing_library,
     }
     return params
 
@@ -87,6 +92,7 @@ def segment_subject_t2_auto_estimate_alveus_ml_cargs(
     """
     cargs = []
     cargs.append("segmentSubjectT2_autoEstimateAlveusML")
+    cargs.append(params.get("missing_library"))
     return cargs
 
 
@@ -134,6 +140,7 @@ def segment_subject_t2_auto_estimate_alveus_ml_execute(
 
 
 def segment_subject_t2_auto_estimate_alveus_ml(
+    missing_library: str = "libmwlaunchermain.so: cannot open shared object file",
     runner: Runner | None = None,
 ) -> SegmentSubjectT2AutoEstimateAlveusMlOutputs:
     """
@@ -144,6 +151,8 @@ def segment_subject_t2_auto_estimate_alveus_ml(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        missing_library: The tool could not be executed due to a missing shared\
+            library: libmwlaunchermain.so.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT2AutoEstimateAlveusMlOutputs`).
@@ -151,6 +160,7 @@ def segment_subject_t2_auto_estimate_alveus_ml(
     runner = runner or get_global_runner()
     execution = runner.start_execution(SEGMENT_SUBJECT_T2_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = segment_subject_t2_auto_estimate_alveus_ml_params(
+        missing_library=missing_library,
     )
     return segment_subject_t2_auto_estimate_alveus_ml_execute(params, execution)
 

niwrap_freesurfer/freesurfer/segpons.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGPONS_METADATA = Metadata(
-    id="4b38e194fdd9fe1d16fc15d6ac746b2dffa56e0f.boutiques",
+    id="8eb6baa748bcc4187afc21f69060f662b9b141d7.boutiques",
     name="segpons",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -118,7 +118,7 @@ def segpons_cargs(
     cargs.append("segpons")
     cargs.extend([
         "-s",
-        "-" + params.get("subject")
+        params.get("subject")
     ])
     if params.get("aseg"):
         cargs.append("--aseg")

niwrap_freesurfer/freesurfer/sphere_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPHERE_SUBJECT_LH_METADATA = Metadata(
-    id="6cb29acf4c0a72caae7b4c3b000c37495ed423e6.boutiques",
+    id="951f794e9569d4f1b767c4b13b886e42c3d32956.boutiques",
     name="sphere_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def sphere_subject_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("sphere_subject-lh")
     cargs.extend([
         "-lh",
-        "sphere_subject" + execution.input_file(params.get("license_file"))
+        execution.input_file(params.get("license_file"))
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/sphere_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPHERE_SUBJECT_RH_METADATA = Metadata(
-    id="844b29d70c1496f2da433daa0b47df80e286dc3b.boutiques",
+    id="3f5f7069b0a16e269b65f3d28ad8762b4bb84b90.boutiques",
     name="sphere_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -91,9 +91,10 @@ def sphere_subject_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("sphere_subject-rh")
     cargs.extend([
         "-rh",
-        "sphere_subject" + execution.input_file(params.get("license_file"))
+        execution.input_file(params.get("license_file"))
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/talairach.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH_METADATA = Metadata(
-    id="1512333dd2617cccb8f9ea33a7bc7b56b8c724e3.boutiques",
+    id="fdcf0b0c4d49174cda1f651aa6a291f3c7d090a9.boutiques",
     name="talairach",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -105,14 +105,14 @@ def talairach_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_nu_correct.mni")
+    cargs.append("talairach")
     cargs.extend([
         "-i",
-        "-" + execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume"))
     ])
     cargs.extend([
         "-xfm",
-        "-" + params.get("output_transform")
+        params.get("output_transform")
     ])
     if params.get("log_flag"):
         cargs.append("--log")