niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_cvs_data_copy.py

@@ -0,0 +1,219 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_CVS_DATA_COPY_METADATA = Metadata(
+    id="b73336351ee9c11ffda39c6ee8b2af17a54695d1.boutiques",
+    name="mri_cvs_data_copy",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriCvsDataCopyParameters = typing.TypedDict('MriCvsDataCopyParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_cvs_data_copy"],
+    "subjid": str,
+    "olddir": str,
+    "newdir": str,
+    "version": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_cvs_data_copy": mri_cvs_data_copy_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 {
+    }.get(t)
+
+
+class MriCvsDataCopyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_cvs_data_copy(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_cvs_data_copy_params(
+    subjid: str,
+    olddir: str,
+    newdir: str,
+    version: bool = False,
+    help_: bool = False,
+) -> MriCvsDataCopyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjid: Subject ID of the subject to be moved/registered.
+        olddir: Directory where data (FS reconned output files for the subject)\
+            is currently located. Use full path.
+        newdir: Directory where data (FS reconned output files for the subject)\
+            should be moved to. Use full path.
+        version: Print version and exit.
+        help_: Print help and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_cvs_data_copy",
+        "subjid": subjid,
+        "olddir": olddir,
+        "newdir": newdir,
+        "version": version,
+        "help": help_,
+    }
+    return params
+
+
+def mri_cvs_data_copy_cargs(
+    params: MriCvsDataCopyParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_cvs_data_copy")
+    cargs.extend([
+        "--subjid",
+        params.get("subjid")
+    ])
+    cargs.extend([
+        "--olddir",
+        params.get("olddir")
+    ])
+    cargs.extend([
+        "--newdir",
+        params.get("newdir")
+    ])
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("help"):
+        cargs.append("--help")
+    return cargs
+
+
+def mri_cvs_data_copy_outputs(
+    params: MriCvsDataCopyParameters,
+    execution: Execution,
+) -> MriCvsDataCopyOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriCvsDataCopyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_cvs_data_copy_execute(
+    params: MriCvsDataCopyParameters,
+    execution: Execution,
+) -> MriCvsDataCopyOutputs:
+    """
+    Packs and copies files that are required for mri_cvs_register.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriCvsDataCopyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_cvs_data_copy_cargs(params, execution)
+    ret = mri_cvs_data_copy_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_cvs_data_copy(
+    subjid: str,
+    olddir: str,
+    newdir: str,
+    version: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MriCvsDataCopyOutputs:
+    """
+    Packs and copies files that are required for mri_cvs_register.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjid: Subject ID of the subject to be moved/registered.
+        olddir: Directory where data (FS reconned output files for the subject)\
+            is currently located. Use full path.
+        newdir: Directory where data (FS reconned output files for the subject)\
+            should be moved to. Use full path.
+        version: Print version and exit.
+        help_: Print help and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriCvsDataCopyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CVS_DATA_COPY_METADATA)
+    params = mri_cvs_data_copy_params(
+        subjid=subjid,
+        olddir=olddir,
+        newdir=newdir,
+        version=version,
+        help_=help_,
+    )
+    return mri_cvs_data_copy_execute(params, execution)
+
+
+__all__ = [
+    "MRI_CVS_DATA_COPY_METADATA",
+    "MriCvsDataCopyOutputs",
+    "MriCvsDataCopyParameters",
+    "mri_cvs_data_copy",
+    "mri_cvs_data_copy_params",
+]

niwrap_freesurfer/freesurfer/mri_cvs_register.py

@@ -0,0 +1,480 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_CVS_REGISTER_METADATA = Metadata(
+    id="bb0813a0151b53cc7fd810cb07043b52e37cd609.boutiques",
+    name="mri_cvs_register",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriCvsRegisterParameters = typing.TypedDict('MriCvsRegisterParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_cvs_register"],
+    "mov_subjid": str,
+    "template_subjid": typing.NotRequired[str | None],
+    "templatedir": typing.NotRequired[str | None],
+    "mni_flag": bool,
+    "outdir": typing.NotRequired[str | None],
+    "asegfname": typing.NotRequired[str | None],
+    "voltype": typing.NotRequired[str | None],
+    "step1_flag": bool,
+    "step2_flag": bool,
+    "step3_flag": bool,
+    "noaseg_flag": bool,
+    "nointensity_flag": bool,
+    "hemi_flag": bool,
+    "masktargethemi_flag": bool,
+    "maskmovinghemi_flag": bool,
+    "nocleanup_flag": bool,
+    "keepelreg_flag": bool,
+    "keepallm3z_flag": bool,
+    "cleanall_flag": bool,
+    "cleansurfreg_flag": bool,
+    "cleanelreg_flag": bool,
+    "cleanvolreg_flag": bool,
+    "m3d_flag": bool,
+    "openmp": typing.NotRequired[int | None],
+    "nolog_flag": bool,
+    "version_flag": bool,
+    "help_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 {
+        "mri_cvs_register": mri_cvs_register_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 {
+        "mri_cvs_register": mri_cvs_register_outputs,
+    }.get(t)
+
+
+class MriCvsRegisterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_cvs_register(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    final_cvs_morph: OutputPathType | None
+    """The final morph that combines correspondences recovered in all
+    registration steps."""
+    final_cvs_morphed_norm: OutputPathType | None
+    """The CVS morphed norm.mgz file; final result of CVS with all registration
+    steps contributions."""
+    final_cvs_morphed_aseg: OutputPathType | None
+    """The CVS morphed aseg.mgz file with all registration steps
+    contributions."""
+    step1_morphed_aseg: OutputPathType | None
+    """Morphed aseg.mgz file result of CVS up to step (3)(i) and contains elatic
+    morph and aseg-based nonlinear registration."""
+    step1_morphed_norm: OutputPathType | None
+    """Morphed norm.mgz file result of CVS up to step (3)(i) and contains elatic
+    morph and aseg-based nonlinear registration."""
+
+
+def mri_cvs_register_params(
+    mov_subjid: str,
+    template_subjid: str | None = None,
+    templatedir: str | None = None,
+    mni_flag: bool = False,
+    outdir: str | None = None,
+    asegfname: str | None = None,
+    voltype: str | None = None,
+    step1_flag: bool = False,
+    step2_flag: bool = False,
+    step3_flag: bool = False,
+    noaseg_flag: bool = False,
+    nointensity_flag: bool = False,
+    hemi_flag: bool = False,
+    masktargethemi_flag: bool = False,
+    maskmovinghemi_flag: bool = False,
+    nocleanup_flag: bool = False,
+    keepelreg_flag: bool = False,
+    keepallm3z_flag: bool = False,
+    cleanall_flag: bool = False,
+    cleansurfreg_flag: bool = False,
+    cleanelreg_flag: bool = False,
+    cleanvolreg_flag: bool = False,
+    m3d_flag: bool = False,
+    openmp: int | None = None,
+    nolog_flag: bool = False,
+    version_flag: bool = False,
+    help_flag: bool = False,
+) -> MriCvsRegisterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        mov_subjid: FreeSurfer subject name as found in $SUBJECTS_DIR. This\
+            identifies the subject that is to be moved / registered to the target.
+        template_subjid: FreeSurfer subject name as found in $SUBJECTS_DIR (or\
+            --templatedir). This identifies the subject that is to be kept fixed\
+            (template).
+        templatedir: Directory of the template subject's SUBJECTS_DIR if\
+            different from that of the moving subject.
+        mni_flag: Use the CVS atlas in MNI152 space as a target for\
+            registration.
+        outdir: Name of the output directory where all the registration results\
+            are written.
+        asegfname: Name of the segmentation volume used in volumetric\
+            registration step. Do not use the file extension.
+        voltype: Changes the input from norm.mgz to voltype.mgz.
+        step1_flag: Only do step 1 (spherical registration).
+        step2_flag: Only do step 2 (elastic registration).
+        step3_flag: Only do step 3 (volumetric registration).
+        noaseg_flag: Do not use aseg volumes in the volumetric registration\
+            pipeline.
+        nointensity_flag: Do not use intensity volumes in the volumetric\
+            registration pipeline.
+        hemi_flag: Run CVS registration only on one hemisphere.
+        masktargethemi_flag: Use with --hemi when hemi is registered to full\
+            brain target.
+        maskmovinghemi_flag: Use with --hemi when full brain is registered to\
+            single hemi target.
+        nocleanup_flag: Do not delete temporary files.
+        keepelreg_flag: Do not delete elastic registration outcomes.
+        keepallm3z_flag: Do not delete m3z morph files computed during CVS.
+        cleanall_flag: Overwrite / recompute all CVS-related morphs.
+        cleansurfreg_flag: Overwrite/recompute CVS-related surface registration\
+            morphs.
+        cleanelreg_flag: Overwrite / recompute CVS-related elastic registration\
+            morph.
+        cleanvolreg_flag: Overwrite / recompute CVS-related volumetric morphs.
+        m3d_flag: Use m3d instead of m3z for registration morphs.
+        openmp: Assign the number of nodes for openmp runs.
+        nolog_flag: Do not produce a log file.
+        version_flag: Print version and exit.
+        help_flag: Print help and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_cvs_register",
+        "mov_subjid": mov_subjid,
+        "mni_flag": mni_flag,
+        "step1_flag": step1_flag,
+        "step2_flag": step2_flag,
+        "step3_flag": step3_flag,
+        "noaseg_flag": noaseg_flag,
+        "nointensity_flag": nointensity_flag,
+        "hemi_flag": hemi_flag,
+        "masktargethemi_flag": masktargethemi_flag,
+        "maskmovinghemi_flag": maskmovinghemi_flag,
+        "nocleanup_flag": nocleanup_flag,
+        "keepelreg_flag": keepelreg_flag,
+        "keepallm3z_flag": keepallm3z_flag,
+        "cleanall_flag": cleanall_flag,
+        "cleansurfreg_flag": cleansurfreg_flag,
+        "cleanelreg_flag": cleanelreg_flag,
+        "cleanvolreg_flag": cleanvolreg_flag,
+        "m3d_flag": m3d_flag,
+        "nolog_flag": nolog_flag,
+        "version_flag": version_flag,
+        "help_flag": help_flag,
+    }
+    if template_subjid is not None:
+        params["template_subjid"] = template_subjid
+    if templatedir is not None:
+        params["templatedir"] = templatedir
+    if outdir is not None:
+        params["outdir"] = outdir
+    if asegfname is not None:
+        params["asegfname"] = asegfname
+    if voltype is not None:
+        params["voltype"] = voltype
+    if openmp is not None:
+        params["openmp"] = openmp
+    return params
+
+
+def mri_cvs_register_cargs(
+    params: MriCvsRegisterParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_cvs_register")
+    cargs.extend([
+        "--mov",
+        params.get("mov_subjid")
+    ])
+    if params.get("template_subjid") is not None:
+        cargs.extend([
+            "--template",
+            params.get("template_subjid")
+        ])
+    if params.get("templatedir") is not None:
+        cargs.extend([
+            "--templatedir",
+            params.get("templatedir")
+        ])
+    if params.get("mni_flag"):
+        cargs.append("--mni")
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "--outdir",
+            params.get("outdir")
+        ])
+    if params.get("asegfname") is not None:
+        cargs.extend([
+            "--asegfname",
+            params.get("asegfname")
+        ])
+    if params.get("voltype") is not None:
+        cargs.extend([
+            "--voltype",
+            params.get("voltype")
+        ])
+    if params.get("step1_flag"):
+        cargs.append("--step1")
+    if params.get("step2_flag"):
+        cargs.append("--step2")
+    if params.get("step3_flag"):
+        cargs.append("--step3")
+    if params.get("noaseg_flag"):
+        cargs.append("--noaseg")
+    if params.get("nointensity_flag"):
+        cargs.append("--nointensity")
+    if params.get("hemi_flag"):
+        cargs.append("--hemi")
+    if params.get("masktargethemi_flag"):
+        cargs.append("--masktargethemi")
+    if params.get("maskmovinghemi_flag"):
+        cargs.append("--maskmovinghemi")
+    if params.get("nocleanup_flag"):
+        cargs.append("--nocleanup")
+    if params.get("keepelreg_flag"):
+        cargs.append("--keepelreg")
+    if params.get("keepallm3z_flag"):
+        cargs.append("--keepallm3z")
+    if params.get("cleanall_flag"):
+        cargs.append("--cleanall")
+    if params.get("cleansurfreg_flag"):
+        cargs.append("--cleansurfreg")
+    if params.get("cleanelreg_flag"):
+        cargs.append("--cleanelreg")
+    if params.get("cleanvolreg_flag"):
+        cargs.append("--cleanvolreg")
+    if params.get("m3d_flag"):
+        cargs.append("--m3d")
+    if params.get("openmp") is not None:
+        cargs.extend([
+            "--openmp",
+            str(params.get("openmp"))
+        ])
+    if params.get("nolog_flag"):
+        cargs.append("--nolog")
+    if params.get("version_flag"):
+        cargs.append("--version")
+    if params.get("help_flag"):
+        cargs.append("--help")
+    return cargs
+
+
+def mri_cvs_register_outputs(
+    params: MriCvsRegisterParameters,
+    execution: Execution,
+) -> MriCvsRegisterOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriCvsRegisterOutputs(
+        root=execution.output_file("."),
+        final_cvs_morph=execution.output_file(params.get("outdir") + "/final_CVSmorph_toTEMPLATE.m3z") if (params.get("outdir") is not None) else None,
+        final_cvs_morphed_norm=execution.output_file(params.get("outdir") + "/final_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
+        final_cvs_morphed_aseg=execution.output_file(params.get("outdir") + "/final_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
+        step1_morphed_aseg=execution.output_file(params.get("outdir") + "/step1_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
+        step1_morphed_norm=execution.output_file(params.get("outdir") + "/step1_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
+    )
+    return ret
+
+
+def mri_cvs_register_execute(
+    params: MriCvsRegisterParameters,
+    execution: Execution,
+) -> MriCvsRegisterOutputs:
+    """
+    Combined Volume and Surface Registration.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriCvsRegisterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_cvs_register_cargs(params, execution)
+    ret = mri_cvs_register_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_cvs_register(
+    mov_subjid: str,
+    template_subjid: str | None = None,
+    templatedir: str | None = None,
+    mni_flag: bool = False,
+    outdir: str | None = None,
+    asegfname: str | None = None,
+    voltype: str | None = None,
+    step1_flag: bool = False,
+    step2_flag: bool = False,
+    step3_flag: bool = False,
+    noaseg_flag: bool = False,
+    nointensity_flag: bool = False,
+    hemi_flag: bool = False,
+    masktargethemi_flag: bool = False,
+    maskmovinghemi_flag: bool = False,
+    nocleanup_flag: bool = False,
+    keepelreg_flag: bool = False,
+    keepallm3z_flag: bool = False,
+    cleanall_flag: bool = False,
+    cleansurfreg_flag: bool = False,
+    cleanelreg_flag: bool = False,
+    cleanvolreg_flag: bool = False,
+    m3d_flag: bool = False,
+    openmp: int | None = None,
+    nolog_flag: bool = False,
+    version_flag: bool = False,
+    help_flag: bool = False,
+    runner: Runner | None = None,
+) -> MriCvsRegisterOutputs:
+    """
+    Combined Volume and Surface Registration.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        mov_subjid: FreeSurfer subject name as found in $SUBJECTS_DIR. This\
+            identifies the subject that is to be moved / registered to the target.
+        template_subjid: FreeSurfer subject name as found in $SUBJECTS_DIR (or\
+            --templatedir). This identifies the subject that is to be kept fixed\
+            (template).
+        templatedir: Directory of the template subject's SUBJECTS_DIR if\
+            different from that of the moving subject.
+        mni_flag: Use the CVS atlas in MNI152 space as a target for\
+            registration.
+        outdir: Name of the output directory where all the registration results\
+            are written.
+        asegfname: Name of the segmentation volume used in volumetric\
+            registration step. Do not use the file extension.
+        voltype: Changes the input from norm.mgz to voltype.mgz.
+        step1_flag: Only do step 1 (spherical registration).
+        step2_flag: Only do step 2 (elastic registration).
+        step3_flag: Only do step 3 (volumetric registration).
+        noaseg_flag: Do not use aseg volumes in the volumetric registration\
+            pipeline.
+        nointensity_flag: Do not use intensity volumes in the volumetric\
+            registration pipeline.
+        hemi_flag: Run CVS registration only on one hemisphere.
+        masktargethemi_flag: Use with --hemi when hemi is registered to full\
+            brain target.
+        maskmovinghemi_flag: Use with --hemi when full brain is registered to\
+            single hemi target.
+        nocleanup_flag: Do not delete temporary files.
+        keepelreg_flag: Do not delete elastic registration outcomes.
+        keepallm3z_flag: Do not delete m3z morph files computed during CVS.
+        cleanall_flag: Overwrite / recompute all CVS-related morphs.
+        cleansurfreg_flag: Overwrite/recompute CVS-related surface registration\
+            morphs.
+        cleanelreg_flag: Overwrite / recompute CVS-related elastic registration\
+            morph.
+        cleanvolreg_flag: Overwrite / recompute CVS-related volumetric morphs.
+        m3d_flag: Use m3d instead of m3z for registration morphs.
+        openmp: Assign the number of nodes for openmp runs.
+        nolog_flag: Do not produce a log file.
+        version_flag: Print version and exit.
+        help_flag: Print help and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriCvsRegisterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CVS_REGISTER_METADATA)
+    params = mri_cvs_register_params(
+        mov_subjid=mov_subjid,
+        template_subjid=template_subjid,
+        templatedir=templatedir,
+        mni_flag=mni_flag,
+        outdir=outdir,
+        asegfname=asegfname,
+        voltype=voltype,
+        step1_flag=step1_flag,
+        step2_flag=step2_flag,
+        step3_flag=step3_flag,
+        noaseg_flag=noaseg_flag,
+        nointensity_flag=nointensity_flag,
+        hemi_flag=hemi_flag,
+        masktargethemi_flag=masktargethemi_flag,
+        maskmovinghemi_flag=maskmovinghemi_flag,
+        nocleanup_flag=nocleanup_flag,
+        keepelreg_flag=keepelreg_flag,
+        keepallm3z_flag=keepallm3z_flag,
+        cleanall_flag=cleanall_flag,
+        cleansurfreg_flag=cleansurfreg_flag,
+        cleanelreg_flag=cleanelreg_flag,
+        cleanvolreg_flag=cleanvolreg_flag,
+        m3d_flag=m3d_flag,
+        openmp=openmp,
+        nolog_flag=nolog_flag,
+        version_flag=version_flag,
+        help_flag=help_flag,
+    )
+    return mri_cvs_register_execute(params, execution)
+
+
+__all__ = [
+    "MRI_CVS_REGISTER_METADATA",
+    "MriCvsRegisterOutputs",
+    "MriCvsRegisterParameters",
+    "mri_cvs_register",
+    "mri_cvs_register_params",
+]