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

niwrap_freesurfer/freesurfer/__init__.py

@@ -36,7 +36,6 @@ from .bblabel import *
 from .bbmask import *
 from .bbregister import *
 from .bedpostx_mgh import *
-from .bet_fsl import *
 from .beta2sxa import *
 from .biasfield import *
 from .bmedits2surf import *
@@ -90,7 +89,6 @@ from .dmri_trk2trk import *
 from .dmri_violin_plots import *
 from .dmri_vox2vox import *
 from .dt_recon import *
-from .epidewarp_fsl import *
 from .export_gcam import *
 from .extract_seg_waveform import *
 from .exvivo_hemi_proc import *
@@ -104,7 +102,6 @@ from .fix_subject_corrected_rh import *
 from .fix_subject_rh import *
 from .fixup_mni_paths import *
 from .flip_4dfp import *
-from .flirt_fsl import *
 from .flirt_newdefault_20080811_sch import *
 from .fname2ext import *
 from .fname2stem import *
@@ -121,19 +118,13 @@ from .fs_time import *
 from .fs_tutorial_data import *
 from .fs_update import *
 from .fscalc import *
-from .fscalc_fsl import *
 from .fsdcmdecompress import *
-from .fsfirst_fsl import *
 from .fsl_5_0_2_xyztrans_sch import *
 from .fsl_label2voxel import *
 from .fsl_rigid_register import *
 from .fsl_sub_mgh import *
-from .fslmaths_fsl import *
-from .fslorient_fsl import *
 from .fslregister import *
-from .fslswapdim_fsl import *
 from .fspalm import *
-from .fspython import *
 from .fsr_coreg import *
 from .fsr_getxopts import *
 from .fsr_import import *
@@ -361,7 +352,6 @@ from .mri_modify import *
 from .mri_morphology import *
 from .mri_motion_correct import *
 from .mri_motion_correct2 import *
-from .mri_motion_correct_fsl import *
 from .mri_ms_fitparms import *
 from .mri_nl_align import *
 from .mri_nl_align_binary import *
@@ -652,7 +642,6 @@ from .segpons import *
 from .setlabelstat import *
 from .sfa2fieldsign import *
 from .slicedelay import *
-from .slicetimer_fsl import *
 from .sphere_subject import *
 from .sphere_subject_lh import *
 from .sphere_subject_rh import *

niwrap_freesurfer/freesurfer/annot2std.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANNOT2STD_METADATA = Metadata(
-    id="fcdd66f979c54df988b9364c89c1d5056e322ab6.boutiques",
+    id="2c9123403463828b0f1e87c964b86cb68c130b07.boutiques",
     name="annot2std",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -20,11 +20,14 @@ Annot2stdParameters = typing.TypedDict('Annot2stdParameters', {
     "fsgd_file": typing.NotRequired[InputPathType | None],
     "subject_list_file": typing.NotRequired[InputPathType | None],
     "target": typing.NotRequired[str | None],
+    "left_hemisphere": bool,
     "right_hemisphere": bool,
     "xhemi": bool,
     "surfreg": typing.NotRequired[str | None],
     "srcsurfreg": typing.NotRequired[str | None],
     "trgsurfreg": typing.NotRequired[str | None],
+    "annotname": typing.NotRequired[str | None],
+    "aparc": bool,
     "a2009s": bool,
     "segmentation": typing.NotRequired[str | None],
     "stack": typing.NotRequired[str | None],
@@ -85,11 +88,14 @@ def annot2std_params(
     fsgd_file: InputPathType | None = None,
     subject_list_file: InputPathType | None = None,
     target: str | None = None,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     xhemi: bool = False,
     surfreg: str | None = None,
     srcsurfreg: str | None = None,
     trgsurfreg: str | None = None,
+    annotname: str | None = None,
+    aparc: bool = False,
     a2009s: bool = False,
     segmentation: str | None = None,
     stack: str | None = None,
@@ -106,11 +112,14 @@ def annot2std_params(
         fsgd_file: FSGD file for group descriptor.
         subject_list_file: Subject list file.
         target: Target subject (e.g., fsaverage).
+        left_hemisphere: Use left hemisphere.
         right_hemisphere: Use right hemisphere.
         xhemi: For interhemispheric analysis.
         surfreg: Surface registration type (default is sphere.reg).
         srcsurfreg: Source surface registration type (default is sphere.reg).
         trgsurfreg: Target surface registration type (default is sphere.reg).
+        annotname: Input annotation name (?h.annotname.annot).
+        aparc: Annotation name set to aparc.
         a2009s: Annotation name set to aparc.a2009s.
         segmentation: Save output as a surface segmentation (2 frames, second =\
             p).
@@ -124,8 +133,10 @@ def annot2std_params(
         "__STYXTYPE__": "annot2std",
         "output_annot_path": output_annot_path,
         "subjects": subjects,
+        "left_hemisphere": left_hemisphere,
         "right_hemisphere": right_hemisphere,
         "xhemi": xhemi,
+        "aparc": aparc,
         "a2009s": a2009s,
         "help": help_,
         "version": version,
@@ -142,6 +153,8 @@ def annot2std_params(
         params["srcsurfreg"] = srcsurfreg
     if trgsurfreg is not None:
         params["trgsurfreg"] = trgsurfreg
+    if annotname is not None:
+        params["annotname"] = annotname
     if segmentation is not None:
         params["segmentation"] = segmentation
     if stack is not None:
@@ -187,6 +200,8 @@ def annot2std_cargs(
             "--t",
             params.get("target")
         ])
+    if params.get("left_hemisphere"):
+        cargs.append("--lh")
     if params.get("right_hemisphere"):
         cargs.append("--rh")
     if params.get("xhemi"):
@@ -206,6 +221,13 @@ def annot2std_cargs(
             "--trgsurfreg",
             params.get("trgsurfreg")
         ])
+    if params.get("annotname") is not None:
+        cargs.extend([
+            "--a",
+            params.get("annotname")
+        ])
+    if params.get("aparc"):
+        cargs.append("--aparc")
     if params.get("a2009s"):
         cargs.append("--a2009s")
     if params.get("segmentation") is not None:
@@ -279,11 +301,14 @@ def annot2std(
     fsgd_file: InputPathType | None = None,
     subject_list_file: InputPathType | None = None,
     target: str | None = None,
+    left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     xhemi: bool = False,
     surfreg: str | None = None,
     srcsurfreg: str | None = None,
     trgsurfreg: str | None = None,
+    annotname: str | None = None,
+    aparc: bool = False,
     a2009s: bool = False,
     segmentation: str | None = None,
     stack: str | None = None,
@@ -307,11 +332,14 @@ def annot2std(
         fsgd_file: FSGD file for group descriptor.
         subject_list_file: Subject list file.
         target: Target subject (e.g., fsaverage).
+        left_hemisphere: Use left hemisphere.
         right_hemisphere: Use right hemisphere.
         xhemi: For interhemispheric analysis.
         surfreg: Surface registration type (default is sphere.reg).
         srcsurfreg: Source surface registration type (default is sphere.reg).
         trgsurfreg: Target surface registration type (default is sphere.reg).
+        annotname: Input annotation name (?h.annotname.annot).
+        aparc: Annotation name set to aparc.
         a2009s: Annotation name set to aparc.a2009s.
         segmentation: Save output as a surface segmentation (2 frames, second =\
             p).
@@ -330,11 +358,14 @@ def annot2std(
         fsgd_file=fsgd_file,
         subject_list_file=subject_list_file,
         target=target,
+        left_hemisphere=left_hemisphere,
         right_hemisphere=right_hemisphere,
         xhemi=xhemi,
         surfreg=surfreg,
         srcsurfreg=srcsurfreg,
         trgsurfreg=trgsurfreg,
+        annotname=annotname,
+        aparc=aparc,
         a2009s=a2009s,
         segmentation=segmentation,
         stack=stack,

niwrap_freesurfer/freesurfer/aparc2feat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APARC2FEAT_METADATA = Metadata(
-    id="40a686bfd13826d8c5472e46b643ff5ee20464a4.boutiques",
+    id="0ac9c7d7d17f6bd66cfbc4ec10b36ae576f35039.boutiques",
     name="aparc2feat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -22,6 +22,8 @@ Aparc2featParameters = typing.TypedDict('Aparc2featParameters', {
     "annot_a2005s_flag": bool,
     "annot_a2009s_flag": bool,
     "debug_flag": bool,
+    "help_flag": bool,
+    "version_flag": bool,
 })
 
 
@@ -77,6 +79,8 @@ def aparc2feat_params(
     annot_a2005s_flag: bool = False,
     annot_a2009s_flag: bool = False,
     debug_flag: bool = False,
+    help_flag: bool = False,
+    version_flag: bool = False,
 ) -> Aparc2featParameters:
     """
     Build parameters.
@@ -91,6 +95,8 @@ def aparc2feat_params(
         annot_a2005s_flag: Specify annotation = aparc.a2005s.
         annot_a2009s_flag: Specify annotation = aparc.a2009s.
         debug_flag: Turn on debugging.
+        help_flag: Print help and exit.
+        version_flag: Print version and exit.
     Returns:
         Parameter dictionary
     """
@@ -100,6 +106,8 @@ def aparc2feat_params(
         "annot_a2005s_flag": annot_a2005s_flag,
         "annot_a2009s_flag": annot_a2009s_flag,
         "debug_flag": debug_flag,
+        "help_flag": help_flag,
+        "version_flag": version_flag,
     }
     if featdirfile is not None:
         params["featdirfile"] = featdirfile
@@ -150,6 +158,10 @@ def aparc2feat_cargs(
         cargs.append("--a2009s")
     if params.get("debug_flag"):
         cargs.append("--debug")
+    if params.get("help_flag"):
+        cargs.append("--help")
+    if params.get("version_flag"):
+        cargs.append("--version")
     return cargs
 
 
@@ -207,6 +219,8 @@ def aparc2feat(
     annot_a2005s_flag: bool = False,
     annot_a2009s_flag: bool = False,
     debug_flag: bool = False,
+    help_flag: bool = False,
+    version_flag: bool = False,
     runner: Runner | None = None,
 ) -> Aparc2featOutputs:
     """
@@ -227,6 +241,8 @@ def aparc2feat(
         annot_a2005s_flag: Specify annotation = aparc.a2005s.
         annot_a2009s_flag: Specify annotation = aparc.a2009s.
         debug_flag: Turn on debugging.
+        help_flag: Print help and exit.
+        version_flag: Print version and exit.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Aparc2featOutputs`).
@@ -241,6 +257,8 @@ def aparc2feat(
         annot_a2005s_flag=annot_a2005s_flag,
         annot_a2009s_flag=annot_a2009s_flag,
         debug_flag=debug_flag,
+        help_flag=help_flag,
+        version_flag=version_flag,
     )
     return aparc2feat_execute(params, execution)
 

niwrap_freesurfer/freesurfer/bbregister.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BBREGISTER_METADATA = Metadata(
-    id="06a9a3d42999005484cd3e30d110e491b2d7dca8.boutiques",
+    id="dc717dfae108a6dd8224d23542be08c7135f2602.boutiques",
     name="bbregister",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,7 +18,19 @@ BbregisterParameters = typing.TypedDict('BbregisterParameters', {
     "subject": str,
     "moveable_volume": InputPathType,
     "reg_file": str,
+    "contrast_type_t1": bool,
     "contrast_type_t2": bool,
+    "vsm": typing.NotRequired[InputPathType | None],
+    "init_coreg": bool,
+    "no_coreg_ref_mask": bool,
+    "init_header": bool,
+    "init_reg": typing.NotRequired[InputPathType | None],
+    "intvol": typing.NotRequired[InputPathType | None],
+    "mid_frame": bool,
+    "frame_no": typing.NotRequired[float | None],
+    "template_out": typing.NotRequired[str | None],
+    "o_outvol": typing.NotRequired[str | None],
+    "s_from_reg": bool,
 })
 
 
@@ -62,7 +74,7 @@ class BbregisterOutputs(typing.NamedTuple):
     """Output root folder. This is the root folder for all outputs."""
     reg_output: OutputPathType
     """Output registration file in dat or lta format."""
-    out_volume: OutputPathType
+    out_volume: OutputPathType | None
     """Resampled moveable volume."""
 
 
@@ -70,7 +82,19 @@ def bbregister_params(
     subject: str,
     moveable_volume: InputPathType,
     reg_file: str,
+    contrast_type_t1: bool = False,
     contrast_type_t2: bool = False,
+    vsm: InputPathType | None = None,
+    init_coreg: bool = False,
+    no_coreg_ref_mask: bool = False,
+    init_header: bool = False,
+    init_reg: InputPathType | None = None,
+    intvol: InputPathType | None = None,
+    mid_frame: bool = False,
+    frame_no: float | None = None,
+    template_out: str | None = None,
+    o_outvol: str | None = None,
+    s_from_reg: bool = False,
 ) -> BbregisterParameters:
     """
     Build parameters.
@@ -81,8 +105,24 @@ def bbregister_params(
             E.g., fMRI volume used for motion correction.
         reg_file: Output FreeSurfer registration file (tkregister-style or LTA\
             format).
+        contrast_type_t1: Assume T1 contrast, White Matter brighter than Grey\
+            Matter.
         contrast_type_t2: Assume T2 contrast, Grey Matter brighter than White\
             Matter. Same as --bold and --dti.
+        vsm: Include B0 distortion correction. A voxel shift map can be created\
+            with the epidewarp.fsl script.
+        init_coreg: Initialize with FreeSurfer mri_coreg program.
+        no_coreg_ref_mask: Do not use aparc+aseg.mgz as a reference mask.
+        init_header: Use geometry info for close voxel-to-voxel registration.\
+            Typically valid if acquired in same session.
+        init_reg: Supply an initial registration matrix; can be LTA format.
+        intvol: Volume used as an intermediate during registration. Useful for\
+            partial field-of-view volumes.
+        mid_frame: Register to middle frame (not with --frame option).
+        frame_no: Register to specified frame (default is 0=1st).
+        template_out: Save template (beneficial with --frame).
+        o_outvol: Resample moveable volume and save as specified output volume.
+        s_from_reg: Get subject name from registration file.
     Returns:
         Parameter dictionary
     """
@@ -91,8 +131,26 @@ def bbregister_params(
         "subject": subject,
         "moveable_volume": moveable_volume,
         "reg_file": reg_file,
+        "contrast_type_t1": contrast_type_t1,
         "contrast_type_t2": contrast_type_t2,
+        "init_coreg": init_coreg,
+        "no_coreg_ref_mask": no_coreg_ref_mask,
+        "init_header": init_header,
+        "mid_frame": mid_frame,
+        "s_from_reg": s_from_reg,
     }
+    if vsm is not None:
+        params["vsm"] = vsm
+    if init_reg is not None:
+        params["init_reg"] = init_reg
+    if intvol is not None:
+        params["intvol"] = intvol
+    if frame_no is not None:
+        params["frame_no"] = frame_no
+    if template_out is not None:
+        params["template_out"] = template_out
+    if o_outvol is not None:
+        params["o_outvol"] = o_outvol
     return params
 
 
@@ -123,9 +181,50 @@ def bbregister_cargs(
         "--reg",
         params.get("reg_file")
     ])
+    if params.get("contrast_type_t1"):
+        cargs.append("--t1")
     if params.get("contrast_type_t2"):
         cargs.append("--t2")
-    cargs.append("[OPTIONS]")
+    if params.get("vsm") is not None:
+        cargs.extend([
+            "--vsm",
+            execution.input_file(params.get("vsm"))
+        ])
+    if params.get("init_coreg"):
+        cargs.append("--init-coreg")
+    if params.get("no_coreg_ref_mask"):
+        cargs.append("--no-coreg-ref-mask")
+    if params.get("init_header"):
+        cargs.append("--init-header")
+    if params.get("init_reg") is not None:
+        cargs.extend([
+            "--init-reg",
+            execution.input_file(params.get("init_reg"))
+        ])
+    if params.get("intvol") is not None:
+        cargs.extend([
+            "--int",
+            execution.input_file(params.get("intvol"))
+        ])
+    if params.get("mid_frame"):
+        cargs.append("--mid-frame")
+    if params.get("frame_no") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame_no"))
+        ])
+    if params.get("template_out") is not None:
+        cargs.extend([
+            "--template-out",
+            params.get("template_out")
+        ])
+    if params.get("o_outvol") is not None:
+        cargs.extend([
+            "--o",
+            params.get("o_outvol")
+        ])
+    if params.get("s_from_reg"):
+        cargs.append("--s-from-reg")
     return cargs
 
 
@@ -145,7 +244,7 @@ def bbregister_outputs(
     ret = BbregisterOutputs(
         root=execution.output_file("."),
         reg_output=execution.output_file(params.get("reg_file")),
-        out_volume=execution.output_file("[O_OUTVOL]"),
+        out_volume=execution.output_file(params.get("o_outvol")) if (params.get("o_outvol") is not None) else None,
     )
     return ret
 
@@ -179,7 +278,19 @@ def bbregister(
     subject: str,
     moveable_volume: InputPathType,
     reg_file: str,
+    contrast_type_t1: bool = False,
     contrast_type_t2: bool = False,
+    vsm: InputPathType | None = None,
+    init_coreg: bool = False,
+    no_coreg_ref_mask: bool = False,
+    init_header: bool = False,
+    init_reg: InputPathType | None = None,
+    intvol: InputPathType | None = None,
+    mid_frame: bool = False,
+    frame_no: float | None = None,
+    template_out: str | None = None,
+    o_outvol: str | None = None,
+    s_from_reg: bool = False,
     runner: Runner | None = None,
 ) -> BbregisterOutputs:
     """
@@ -196,8 +307,24 @@ def bbregister(
             E.g., fMRI volume used for motion correction.
         reg_file: Output FreeSurfer registration file (tkregister-style or LTA\
             format).
+        contrast_type_t1: Assume T1 contrast, White Matter brighter than Grey\
+            Matter.
         contrast_type_t2: Assume T2 contrast, Grey Matter brighter than White\
             Matter. Same as --bold and --dti.
+        vsm: Include B0 distortion correction. A voxel shift map can be created\
+            with the epidewarp.fsl script.
+        init_coreg: Initialize with FreeSurfer mri_coreg program.
+        no_coreg_ref_mask: Do not use aparc+aseg.mgz as a reference mask.
+        init_header: Use geometry info for close voxel-to-voxel registration.\
+            Typically valid if acquired in same session.
+        init_reg: Supply an initial registration matrix; can be LTA format.
+        intvol: Volume used as an intermediate during registration. Useful for\
+            partial field-of-view volumes.
+        mid_frame: Register to middle frame (not with --frame option).
+        frame_no: Register to specified frame (default is 0=1st).
+        template_out: Save template (beneficial with --frame).
+        o_outvol: Resample moveable volume and save as specified output volume.
+        s_from_reg: Get subject name from registration file.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BbregisterOutputs`).
@@ -208,7 +335,19 @@ def bbregister(
         subject=subject,
         moveable_volume=moveable_volume,
         reg_file=reg_file,
+        contrast_type_t1=contrast_type_t1,
         contrast_type_t2=contrast_type_t2,
+        vsm=vsm,
+        init_coreg=init_coreg,
+        no_coreg_ref_mask=no_coreg_ref_mask,
+        init_header=init_header,
+        init_reg=init_reg,
+        intvol=intvol,
+        mid_frame=mid_frame,
+        frame_no=frame_no,
+        template_out=template_out,
+        o_outvol=o_outvol,
+        s_from_reg=s_from_reg,
     )
     return bbregister_execute(params, execution)
 

niwrap_freesurfer/freesurfer/bmedits2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BMEDITS2SURF_METADATA = Metadata(
-    id="be18624e39ce9efc3a4eb4744be1016b11c9fa5f.boutiques",
+    id="f869eae38aafdf868c159585778d592e90997dbd.boutiques",
     name="bmedits2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -146,7 +146,7 @@ def bmedits2surf_cargs(
     cargs.append("bmedits2surf")
     cargs.extend([
         "-s",
-        "-" + params.get("subject")
+        params.get("subject")
     ])
     if params.get("self"):
         cargs.append("--self")

niwrap_freesurfer/freesurfer/compute_interrater_variability_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA = Metadata(
-    id="d85f89519ecdd6db050cf20b230dd279bab615ca.boutiques",
+    id="7363f7a4d7e7af9a9827c3ca57854bc1610a9623.boutiques",
     name="compute_interrater_variability.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,6 +18,8 @@ ComputeInterraterVariabilityCshParameters = typing.TypedDict('ComputeInterraterV
     "label_vol1": InputPathType,
     "label_vol2": InputPathType,
     "output_prefix": str,
+    "version": bool,
+    "help": bool,
 })
 
 
@@ -72,6 +74,8 @@ def compute_interrater_variability_csh_params(
     label_vol1: InputPathType,
     label_vol2: InputPathType,
     output_prefix: str,
+    version: bool = False,
+    help_: bool = False,
 ) -> ComputeInterraterVariabilityCshParameters:
     """
     Build parameters.
@@ -81,6 +85,8 @@ def compute_interrater_variability_csh_params(
         label_vol2: Label volume from rater 2.
         output_prefix: Prefix for the output text files containing results. A\
             total of three files will be produced.
+        version: Print version information and exit.
+        help_: Print help information and exit.
     Returns:
         Parameter dictionary
     """
@@ -89,6 +95,8 @@ def compute_interrater_variability_csh_params(
         "label_vol1": label_vol1,
         "label_vol2": label_vol2,
         "output_prefix": output_prefix,
+        "version": version,
+        "help": help_,
     }
     return params
 
@@ -107,7 +115,7 @@ def compute_interrater_variability_csh_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("compute_interrater_variability")
+    cargs.append("compute_interrater_variability.csh")
     cargs.extend([
         "--vol1",
         execution.input_file(params.get("label_vol1"))
@@ -120,6 +128,10 @@ def compute_interrater_variability_csh_cargs(
         "--out",
         params.get("output_prefix")
     ])
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("help"):
+        cargs.append("--help")
     return cargs
 
 
@@ -174,6 +186,8 @@ def compute_interrater_variability_csh(
     label_vol1: InputPathType,
     label_vol2: InputPathType,
     output_prefix: str,
+    version: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> ComputeInterraterVariabilityCshOutputs:
     """
@@ -189,6 +203,8 @@ def compute_interrater_variability_csh(
         label_vol2: Label volume from rater 2.
         output_prefix: Prefix for the output text files containing results. A\
             total of three files will be produced.
+        version: Print version information and exit.
+        help_: Print help information and exit.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ComputeInterraterVariabilityCshOutputs`).
@@ -199,6 +215,8 @@ def compute_interrater_variability_csh(
         label_vol1=label_vol1,
         label_vol2=label_vol2,
         output_prefix=output_prefix,
+        version=version,
+        help_=help_,
     )
     return compute_interrater_variability_csh_execute(params, execution)