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

niwrap_freesurfer/freesurfer/lta_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LTA_CONVERT_METADATA = Metadata(
-    id="daaa6767af53c23e0e3f62c31924d12dbc6e0eaa.boutiques",
+    id="089d903b1865bcb03759aa837457f18ed456f5ed.boutiques",
     name="lta_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,7 +15,19 @@ LTA_CONVERT_METADATA = Metadata(
 
 LtaConvertParameters = typing.TypedDict('LtaConvertParameters', {
     "__STYX_TYPE__": typing.Literal["lta_convert"],
+    "in_lta": typing.NotRequired[InputPathType | None],
+    "in_fsl": typing.NotRequired[InputPathType | None],
+    "in_mni": typing.NotRequired[InputPathType | None],
+    "in_reg": typing.NotRequired[InputPathType | None],
+    "in_niftyreg": typing.NotRequired[InputPathType | None],
+    "in_itk": typing.NotRequired[InputPathType | None],
     "in_vox": typing.NotRequired[InputPathType | None],
+    "out_lta": typing.NotRequired[str | None],
+    "out_fsl": typing.NotRequired[str | None],
+    "out_mni": typing.NotRequired[str | None],
+    "out_reg": typing.NotRequired[str | None],
+    "out_niftyreg": typing.NotRequired[str | None],
+    "out_itk": typing.NotRequired[str | None],
     "out_vox": typing.NotRequired[str | None],
     "invert": bool,
     "ltavox2vox": bool,
@@ -70,7 +82,19 @@ class LtaConvertOutputs(typing.NamedTuple):
 
 
 def lta_convert_params(
+    in_lta: InputPathType | None = None,
+    in_fsl: InputPathType | None = None,
+    in_mni: InputPathType | None = None,
+    in_reg: InputPathType | None = None,
+    in_niftyreg: InputPathType | None = None,
+    in_itk: InputPathType | None = None,
     in_vox: InputPathType | None = None,
+    out_lta: str | None = None,
+    out_fsl: str | None = None,
+    out_mni: str | None = None,
+    out_reg: str | None = None,
+    out_niftyreg: str | None = None,
+    out_itk: str | None = None,
     out_vox: str | None = None,
     invert: bool = False,
     ltavox2vox: bool = False,
@@ -84,7 +108,19 @@ def lta_convert_params(
     Build parameters.
     
     Args:
+        in_lta: Input transform of LTA type.
+        in_fsl: Input transform of FSL type.
+        in_mni: Input transform of MNI / XFM type.
+        in_reg: Input transform of TK REG type (deprecated format).
+        in_niftyreg: Input transform of NiftyReg type (inverse RAS2RAS).
+        in_itk: Input ITK transform (inverse LPS2LPS).
         in_vox: Input transform in source image space (inverse VOX2VOX).
+        out_lta: Output linear transform (LTA FreeSurfer format).
+        out_fsl: Output transform in FSL format.
+        out_mni: Output transform in MNI/XFM format.
+        out_reg: Output transform in REG DAT format.
+        out_niftyreg: Output transform in NiftyReg format (inverse RAS2RAS).
+        out_itk: Output transform in ITK TXT format (inverse LPS2LPS).
         out_vox: Output transform in source image space (inverse VOX2VOX).
         invert: Inverts transform.
         ltavox2vox: Output type VOX2VOX (default RAS2RAS) with --ltaout.
@@ -105,8 +141,32 @@ def lta_convert_params(
         "ltatkreg": ltatkreg,
         "trg_conform": trg_conform,
     }
+    if in_lta is not None:
+        params["in_lta"] = in_lta
+    if in_fsl is not None:
+        params["in_fsl"] = in_fsl
+    if in_mni is not None:
+        params["in_mni"] = in_mni
+    if in_reg is not None:
+        params["in_reg"] = in_reg
+    if in_niftyreg is not None:
+        params["in_niftyreg"] = in_niftyreg
+    if in_itk is not None:
+        params["in_itk"] = in_itk
     if in_vox is not None:
         params["in_vox"] = in_vox
+    if out_lta is not None:
+        params["out_lta"] = out_lta
+    if out_fsl is not None:
+        params["out_fsl"] = out_fsl
+    if out_mni is not None:
+        params["out_mni"] = out_mni
+    if out_reg is not None:
+        params["out_reg"] = out_reg
+    if out_niftyreg is not None:
+        params["out_niftyreg"] = out_niftyreg
+    if out_itk is not None:
+        params["out_itk"] = out_itk
     if out_vox is not None:
         params["out_vox"] = out_vox
     if src_geometry is not None:
@@ -133,11 +193,71 @@ def lta_convert_cargs(
     """
     cargs = []
     cargs.append("lta_convert")
+    if params.get("in_lta") is not None:
+        cargs.extend([
+            "--inlta",
+            execution.input_file(params.get("in_lta"))
+        ])
+    if params.get("in_fsl") is not None:
+        cargs.extend([
+            "--infsl",
+            execution.input_file(params.get("in_fsl"))
+        ])
+    if params.get("in_mni") is not None:
+        cargs.extend([
+            "--inmni",
+            execution.input_file(params.get("in_mni"))
+        ])
+    if params.get("in_reg") is not None:
+        cargs.extend([
+            "--inreg",
+            execution.input_file(params.get("in_reg"))
+        ])
+    if params.get("in_niftyreg") is not None:
+        cargs.extend([
+            "--inniftyreg",
+            execution.input_file(params.get("in_niftyreg"))
+        ])
+    if params.get("in_itk") is not None:
+        cargs.extend([
+            "--initk",
+            execution.input_file(params.get("in_itk"))
+        ])
     if params.get("in_vox") is not None:
         cargs.extend([
             "--invox",
             execution.input_file(params.get("in_vox"))
         ])
+    if params.get("out_lta") is not None:
+        cargs.extend([
+            "--outlta",
+            params.get("out_lta")
+        ])
+    if params.get("out_fsl") is not None:
+        cargs.extend([
+            "--outfsl",
+            params.get("out_fsl")
+        ])
+    if params.get("out_mni") is not None:
+        cargs.extend([
+            "--outmni",
+            params.get("out_mni")
+        ])
+    if params.get("out_reg") is not None:
+        cargs.extend([
+            "--outreg",
+            params.get("out_reg")
+        ])
+    if params.get("out_niftyreg") is not None:
+        cargs.extend([
+            "--outniftyreg",
+            params.get("out_niftyreg")
+        ])
+    if params.get("out_itk") is not None:
+        cargs.extend([
+            "--outitk",
+            params.get("out_itk")
+        ])
     if params.get("out_vox") is not None:
         cargs.extend([
             "--outvox",
@@ -214,7 +334,19 @@ def lta_convert_execute(
 
 
 def lta_convert(
+    in_lta: InputPathType | None = None,
+    in_fsl: InputPathType | None = None,
+    in_mni: InputPathType | None = None,
+    in_reg: InputPathType | None = None,
+    in_niftyreg: InputPathType | None = None,
+    in_itk: InputPathType | None = None,
     in_vox: InputPathType | None = None,
+    out_lta: str | None = None,
+    out_fsl: str | None = None,
+    out_mni: str | None = None,
+    out_reg: str | None = None,
+    out_niftyreg: str | None = None,
+    out_itk: str | None = None,
     out_vox: str | None = None,
     invert: bool = False,
     ltavox2vox: bool = False,
@@ -233,7 +365,19 @@ def lta_convert(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        in_lta: Input transform of LTA type.
+        in_fsl: Input transform of FSL type.
+        in_mni: Input transform of MNI / XFM type.
+        in_reg: Input transform of TK REG type (deprecated format).
+        in_niftyreg: Input transform of NiftyReg type (inverse RAS2RAS).
+        in_itk: Input ITK transform (inverse LPS2LPS).
         in_vox: Input transform in source image space (inverse VOX2VOX).
+        out_lta: Output linear transform (LTA FreeSurfer format).
+        out_fsl: Output transform in FSL format.
+        out_mni: Output transform in MNI/XFM format.
+        out_reg: Output transform in REG DAT format.
+        out_niftyreg: Output transform in NiftyReg format (inverse RAS2RAS).
+        out_itk: Output transform in ITK TXT format (inverse LPS2LPS).
         out_vox: Output transform in source image space (inverse VOX2VOX).
         invert: Inverts transform.
         ltavox2vox: Output type VOX2VOX (default RAS2RAS) with --ltaout.
@@ -251,7 +395,19 @@ def lta_convert(
     runner = runner or get_global_runner()
     execution = runner.start_execution(LTA_CONVERT_METADATA)
     params = lta_convert_params(
+        in_lta=in_lta,
+        in_fsl=in_fsl,
+        in_mni=in_mni,
+        in_reg=in_reg,
+        in_niftyreg=in_niftyreg,
+        in_itk=in_itk,
         in_vox=in_vox,
+        out_lta=out_lta,
+        out_fsl=out_fsl,
+        out_mni=out_mni,
+        out_reg=out_reg,
+        out_niftyreg=out_niftyreg,
+        out_itk=out_itk,
         out_vox=out_vox,
         invert=invert,
         ltavox2vox=ltavox2vox,

niwrap_freesurfer/freesurfer/make_average_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_AVERAGE_VOLUME_METADATA = Metadata(
-    id="52d00009c5f5db471f13423dea8699f07efa357d.boutiques",
+    id="72e02e18d338618b963b745c51ee6a0b8c78e972.boutiques",
     name="make_average_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -21,12 +21,14 @@ MakeAverageVolumeParameters = typing.TypedDict('MakeAverageVolumeParameters', {
     "topdir": typing.NotRequired[str | None],
     "xform": typing.NotRequired[str | None],
     "sdir": typing.NotRequired[str | None],
+    "sd_flag": bool,
     "force_flag": bool,
     "keep_all_orig_flag": bool,
     "no_aseg_flag": bool,
     "ctab": typing.NotRequired[str | None],
     "ctab_default_flag": bool,
     "echo_flag": bool,
+    "debug_flag": bool,
     "nocleanup_flag": bool,
 })
 
@@ -77,12 +79,14 @@ def make_average_volume_params(
     topdir: str | None = None,
     xform: str | None = None,
     sdir: str | None = None,
+    sd_flag: bool = False,
     force_flag: bool = False,
     keep_all_orig_flag: bool = False,
     no_aseg_flag: bool = False,
     ctab: str | None = None,
     ctab_default_flag: bool = False,
     echo_flag: bool = False,
+    debug_flag: bool = False,
     nocleanup_flag: bool = False,
 ) -> MakeAverageVolumeParameters:
     """
@@ -95,6 +99,7 @@ def make_average_volume_params(
         topdir: Directory to put data and link to SUBJECTS_DIR.
         xform: Transformation name to use, default is talairach.xfm.
         sdir: Use specified SUBJECTS_DIR instead of the environment's one.
+        sd_flag: Same as --sdir.
         force_flag: Overwrite existing average subject data.
         keep_all_orig_flag: Concatenate all original volumes into\
             mri/orig.all.mgz.
@@ -102,6 +107,7 @@ def make_average_volume_params(
         ctab: Embed colortable into segmentations.
         ctab_default_flag: Embed FreeSurferColorLUT.txt into segmentations.
         echo_flag: Enable command echo for debugging.
+        debug_flag: Same as --echo for debugging.
         nocleanup_flag: Do not delete temporary files.
     Returns:
         Parameter dictionary
@@ -109,11 +115,13 @@ def make_average_volume_params(
     params = {
         "__STYXTYPE__": "make_average_volume",
         "subjects": subjects,
+        "sd_flag": sd_flag,
         "force_flag": force_flag,
         "keep_all_orig_flag": keep_all_orig_flag,
         "no_aseg_flag": no_aseg_flag,
         "ctab_default_flag": ctab_default_flag,
         "echo_flag": echo_flag,
+        "debug_flag": debug_flag,
         "nocleanup_flag": nocleanup_flag,
     }
     if fsgd is not None:
@@ -175,6 +183,8 @@ def make_average_volume_cargs(
             "--sdir",
             params.get("sdir")
         ])
+    if params.get("sd_flag"):
+        cargs.append("--sd")
     if params.get("force_flag"):
         cargs.append("--force")
     if params.get("keep_all_orig_flag"):
@@ -190,6 +200,8 @@ def make_average_volume_cargs(
         cargs.append("--ctab-default")
     if params.get("echo_flag"):
         cargs.append("--echo")
+    if params.get("debug_flag"):
+        cargs.append("--debug")
     if params.get("nocleanup_flag"):
         cargs.append("--nocleanup")
     return cargs
@@ -245,12 +257,14 @@ def make_average_volume(
     topdir: str | None = None,
     xform: str | None = None,
     sdir: str | None = None,
+    sd_flag: bool = False,
     force_flag: bool = False,
     keep_all_orig_flag: bool = False,
     no_aseg_flag: bool = False,
     ctab: str | None = None,
     ctab_default_flag: bool = False,
     echo_flag: bool = False,
+    debug_flag: bool = False,
     nocleanup_flag: bool = False,
     runner: Runner | None = None,
 ) -> MakeAverageVolumeOutputs:
@@ -268,6 +282,7 @@ def make_average_volume(
         topdir: Directory to put data and link to SUBJECTS_DIR.
         xform: Transformation name to use, default is talairach.xfm.
         sdir: Use specified SUBJECTS_DIR instead of the environment's one.
+        sd_flag: Same as --sdir.
         force_flag: Overwrite existing average subject data.
         keep_all_orig_flag: Concatenate all original volumes into\
             mri/orig.all.mgz.
@@ -275,6 +290,7 @@ def make_average_volume(
         ctab: Embed colortable into segmentations.
         ctab_default_flag: Embed FreeSurferColorLUT.txt into segmentations.
         echo_flag: Enable command echo for debugging.
+        debug_flag: Same as --echo for debugging.
         nocleanup_flag: Do not delete temporary files.
         runner: Command runner.
     Returns:
@@ -289,12 +305,14 @@ def make_average_volume(
         topdir=topdir,
         xform=xform,
         sdir=sdir,
+        sd_flag=sd_flag,
         force_flag=force_flag,
         keep_all_orig_flag=keep_all_orig_flag,
         no_aseg_flag=no_aseg_flag,
         ctab=ctab,
         ctab_default_flag=ctab_default_flag,
         echo_flag=echo_flag,
+        debug_flag=debug_flag,
         nocleanup_flag=nocleanup_flag,
     )
     return make_average_volume_execute(params, execution)

niwrap_freesurfer/freesurfer/make_folding_atlas.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_FOLDING_ATLAS_METADATA = Metadata(
-    id="cd742cf69eb865650042165331953a619d588ea9.boutiques",
+    id="2ea9d8d1b60df2ade6f961abd423e6b44d34ffda.boutiques",
     name="make_folding_atlas",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -24,6 +24,7 @@ MakeFoldingAtlasParameters = typing.TypedDict('MakeFoldingAtlasParameters', {
     "init_surf_reg": typing.NotRequired[str | None],
     "init_subject": typing.NotRequired[str | None],
     "no_annot_template": bool,
+    "left_hemisphere": bool,
     "right_hemisphere": bool,
     "lhrh": bool,
     "ico_order": typing.NotRequired[float | None],
@@ -90,6 +91,7 @@ def make_folding_atlas_params(
     init_surf_reg: str | None = None,
     init_subject: str | None = None,
     no_annot_template: bool = False,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     lhrh: bool = False,
     ico_order: float | None = None,
@@ -116,6 +118,7 @@ def make_folding_atlas_params(
             (default sphere.reg).
         init_subject: Create first atlas from subject instead of all subjects.
         no_annot_template: Disable annotation template (good for monkeys).
+        left_hemisphere: Process left hemisphere.
         right_hemisphere: Process right hemisphere.
         lhrh: Process both left and right hemispheres (default).
         ico_order: Icosahedron order; default is 7.
@@ -136,6 +139,7 @@ def make_folding_atlas_params(
         "__STYXTYPE__": "make_folding_atlas",
         "xhemi": xhemi,
         "no_annot_template": no_annot_template,
+        "left_hemisphere": left_hemisphere,
         "right_hemisphere": right_hemisphere,
         "lhrh": lhrh,
         "no_vol_on_last": no_vol_on_last,
@@ -221,6 +225,8 @@ def make_folding_atlas_cargs(
         ])
     if params.get("no_annot_template"):
         cargs.append("--no-annot-template")
+    if params.get("left_hemisphere"):
+        cargs.append("--lh")
     if params.get("right_hemisphere"):
         cargs.append("--rh")
     if params.get("lhrh"):
@@ -307,6 +313,7 @@ def make_folding_atlas(
     init_surf_reg: str | None = None,
     init_subject: str | None = None,
     no_annot_template: bool = False,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     lhrh: bool = False,
     ico_order: float | None = None,
@@ -338,6 +345,7 @@ def make_folding_atlas(
             (default sphere.reg).
         init_subject: Create first atlas from subject instead of all subjects.
         no_annot_template: Disable annotation template (good for monkeys).
+        left_hemisphere: Process left hemisphere.
         right_hemisphere: Process right hemisphere.
         lhrh: Process both left and right hemispheres (default).
         ico_order: Icosahedron order; default is 7.
@@ -367,6 +375,7 @@ def make_folding_atlas(
         init_surf_reg=init_surf_reg,
         init_subject=init_subject,
         no_annot_template=no_annot_template,
+        left_hemisphere=left_hemisphere,
         right_hemisphere=right_hemisphere,
         lhrh=lhrh,
         ico_order=ico_order,

niwrap_freesurfer/freesurfer/map_all_labels_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAP_ALL_LABELS_LH_METADATA = Metadata(
-    id="569f8a45a5f0082dff949fe6bc883e667d21393b.boutiques",
+    id="97a60688b269fc75bd6ea545f965efcd4df1c156.boutiques",
     name="map_all_labels-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -19,6 +19,7 @@ MapAllLabelsLhParameters = typing.TypedDict('MapAllLabelsLhParameters', {
     "fname": str,
     "hemi": str,
     "spherical_surf": InputPathType,
+    "subjects": list[str],
     "output": str,
 })
 
@@ -70,6 +71,7 @@ def map_all_labels_lh_params(
     fname: str,
     hemi: str,
     spherical_surf: InputPathType,
+    subjects: list[str],
     output: str,
 ) -> MapAllLabelsLhParameters:
     """
@@ -81,6 +83,7 @@ def map_all_labels_lh_params(
         fname: The file name to process.
         hemi: The hemisphere to process (usually 'lh' for left hemisphere).
         spherical_surf: The spherical surface file.
+        subjects: List of subjects to process.
         output: Output file.
     Returns:
         Parameter dictionary
@@ -91,6 +94,7 @@ def map_all_labels_lh_params(
         "fname": fname,
         "hemi": hemi,
         "spherical_surf": spherical_surf,
+        "subjects": subjects,
         "output": output,
     }
     return params
@@ -110,14 +114,15 @@ def map_all_labels_lh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("map_all_labels-lh")
     cargs.extend([
         "-lh",
-        "map_all_labels" + params.get("which")
+        params.get("which")
     ])
     cargs.append(params.get("fname"))
     cargs.append(params.get("hemi"))
     cargs.append(execution.input_file(params.get("spherical_surf")))
-    cargs.append("[SUBJECTS...]")
+    cargs.extend(params.get("subjects"))
     cargs.append(params.get("output"))
     return cargs
 
@@ -171,6 +176,7 @@ def map_all_labels_lh(
     fname: str,
     hemi: str,
     spherical_surf: InputPathType,
+    subjects: list[str],
     output: str,
     runner: Runner | None = None,
 ) -> MapAllLabelsLhOutputs:
@@ -187,6 +193,7 @@ def map_all_labels_lh(
         fname: The file name to process.
         hemi: The hemisphere to process (usually 'lh' for left hemisphere).
         spherical_surf: The spherical surface file.
+        subjects: List of subjects to process.
         output: Output file.
         runner: Command runner.
     Returns:
@@ -199,6 +206,7 @@ def map_all_labels_lh(
         fname=fname,
         hemi=hemi,
         spherical_surf=spherical_surf,
+        subjects=subjects,
         output=output,
     )
     return map_all_labels_lh_execute(params, execution)

niwrap_freesurfer/freesurfer/map_central_sulcus.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAP_CENTRAL_SULCUS_METADATA = Metadata(
-    id="13b958f09713b9767ab00695cb856a93c2ef9725.boutiques",
+    id="516b76e8b1ac8749a680661e63215cc41d8c82f4.boutiques",
     name="map_central_sulcus",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -263,7 +263,7 @@ def map_central_sulcus_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("recon-all")
+    cargs.append("map_central_sulcus")
     cargs.extend([
         "-subjid",
         params.get("subjid")