niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_compute_volume_fractions.py

@@ -0,0 +1,482 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_COMPUTE_VOLUME_FRACTIONS_METADATA = Metadata(
+    id="0166823a396772941b111de738d47982e374ec28.boutiques",
+    name="mri_compute_volume_fractions",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriComputeVolumeFractionsParameters = typing.TypedDict('MriComputeVolumeFractionsParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_compute_volume_fractions"],
+    "output_stem": str,
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "regheader": typing.NotRequired[str | None],
+    "usf": typing.NotRequired[float | None],
+    "resolution": typing.NotRequired[float | None],
+    "resmm": typing.NotRequired[float | None],
+    "segmentation_file": typing.NotRequired[InputPathType | None],
+    "wsurf": typing.NotRequired[str | None],
+    "psurf": typing.NotRequired[str | None],
+    "no_aseg": bool,
+    "stackfile": typing.NotRequired[str | None],
+    "gmfile": typing.NotRequired[str | None],
+    "no_fill_csf": bool,
+    "dilation": typing.NotRequired[float | None],
+    "out_seg": typing.NotRequired[str | None],
+    "ttseg": typing.NotRequired[str | None],
+    "ttseg_ctab": typing.NotRequired[str | None],
+    "mgz_format": bool,
+    "mgh_format": bool,
+    "nii_format": bool,
+    "nii_gz_format": bool,
+    "ttype_head": bool,
+    "vg_thresh": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": 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_compute_volume_fractions": mri_compute_volume_fractions_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_compute_volume_fractions": mri_compute_volume_fractions_outputs,
+    }.get(t)
+
+
+class MriComputeVolumeFractionsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_compute_volume_fractions(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_cortex: OutputPathType
+    """Output cortex volume file."""
+    output_subcort_gm: OutputPathType
+    """Output subcortical gray matter volume file."""
+    output_wm: OutputPathType
+    """Output white matter volume file."""
+    output_csf: OutputPathType
+    """Output cerebrospinal fluid volume file."""
+
+
+def mri_compute_volume_fractions_params(
+    output_stem: str,
+    registration_file: InputPathType | None = None,
+    regheader: str | None = None,
+    usf: float | None = None,
+    resolution: float | None = None,
+    resmm: float | None = None,
+    segmentation_file: InputPathType | None = None,
+    wsurf: str | None = None,
+    psurf: str | None = None,
+    no_aseg: bool = False,
+    stackfile: str | None = None,
+    gmfile: str | None = None,
+    no_fill_csf: bool = False,
+    dilation: float | None = None,
+    out_seg: str | None = None,
+    ttseg: str | None = None,
+    ttseg_ctab: str | None = None,
+    mgz_format: bool = False,
+    mgh_format: bool = False,
+    nii_format: bool = False,
+    nii_gz_format: bool = False,
+    ttype_head: bool = False,
+    vg_thresh: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+) -> MriComputeVolumeFractionsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_stem: Output stem for generated files (e.g. cortex, subcort_gm,\
+            wm, csf). Files will be saved with this stem in different formats based\
+            on the selected flags.
+        registration_file: Registration file (can be LTA or reg.dat). If using\
+            reg.dat, a template volume is needed.
+        regheader: Specify the subject for regheader.
+        usf: Set anatomical upsample factor (default is 2).
+        resolution: Resolution setting. Sets USF to round(1/res).
+        resmm: Set functional upsampling resolution (default is\
+            aseg->xsize/(USF)).
+        segmentation_file: Use specified segmentation file instead of aseg.mgz.
+        wsurf: Specify the white surface (default is 'white').
+        psurf: Specify the pial surface (default is 'pial').
+        no_aseg: Do not include aseg in processing (useful for testing).
+        stackfile: Put cortex, subcortical GM, WM, CSF into a single\
+            multi-frame file.
+        gmfile: Put cortex + subcortical GM into a single-frame file.
+        no_fill_csf: Do not attempt to fill voxels surrounding segmentation\
+            with extracerebral CSF segmentation.
+        dilation: For xCSF fill, dilate by specified number (default is 3). Use\
+            -1 to fill the entire volume.
+        out_seg: Save segmentation (after adding xCSF voxels).
+        ttseg: Save tissue type segmentation.
+        ttseg_ctab: Save tissue type segmentation color table.
+        mgz_format: Use MGZ format.
+        mgh_format: Use MGH format.
+        nii_format: Use NII format.
+        nii_gz_format: Use NII.GZ format.
+        ttype_head: Use default+head instead of default tissue type info for\
+            segmentation.
+        vg_thresh: Threshold for 'ERROR: LTAconcat(): LTAs 0 and 1 do not\
+            match'.
+        debug: Turn on debugging mode.
+        checkopts: Do not run anything, just check options and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_compute_volume_fractions",
+        "output_stem": output_stem,
+        "no_aseg": no_aseg,
+        "no_fill_csf": no_fill_csf,
+        "mgz_format": mgz_format,
+        "mgh_format": mgh_format,
+        "nii_format": nii_format,
+        "nii_gz_format": nii_gz_format,
+        "ttype_head": ttype_head,
+        "debug": debug,
+        "checkopts": checkopts,
+    }
+    if registration_file is not None:
+        params["registration_file"] = registration_file
+    if regheader is not None:
+        params["regheader"] = regheader
+    if usf is not None:
+        params["usf"] = usf
+    if resolution is not None:
+        params["resolution"] = resolution
+    if resmm is not None:
+        params["resmm"] = resmm
+    if segmentation_file is not None:
+        params["segmentation_file"] = segmentation_file
+    if wsurf is not None:
+        params["wsurf"] = wsurf
+    if psurf is not None:
+        params["psurf"] = psurf
+    if stackfile is not None:
+        params["stackfile"] = stackfile
+    if gmfile is not None:
+        params["gmfile"] = gmfile
+    if dilation is not None:
+        params["dilation"] = dilation
+    if out_seg is not None:
+        params["out_seg"] = out_seg
+    if ttseg is not None:
+        params["ttseg"] = ttseg
+    if ttseg_ctab is not None:
+        params["ttseg_ctab"] = ttseg_ctab
+    if vg_thresh is not None:
+        params["vg_thresh"] = vg_thresh
+    return params
+
+
+def mri_compute_volume_fractions_cargs(
+    params: MriComputeVolumeFractionsParameters,
+    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_compute_volume_fractions")
+    cargs.extend([
+        "--o",
+        params.get("output_stem")
+    ])
+    if params.get("registration_file") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("registration_file"))
+        ])
+    if params.get("regheader") is not None:
+        cargs.extend([
+            "--regheader",
+            params.get("regheader")
+        ])
+    if params.get("usf") is not None:
+        cargs.extend([
+            "--usf",
+            str(params.get("usf"))
+        ])
+    if params.get("resolution") is not None:
+        cargs.extend([
+            "--r",
+            str(params.get("resolution"))
+        ])
+    if params.get("resmm") is not None:
+        cargs.extend([
+            "--resmm",
+            str(params.get("resmm"))
+        ])
+    if params.get("segmentation_file") is not None:
+        cargs.extend([
+            "--seg",
+            execution.input_file(params.get("segmentation_file"))
+        ])
+    if params.get("wsurf") is not None:
+        cargs.extend([
+            "--wsurf",
+            params.get("wsurf")
+        ])
+    if params.get("psurf") is not None:
+        cargs.extend([
+            "--psurf",
+            params.get("psurf")
+        ])
+    if params.get("no_aseg"):
+        cargs.append("--no-aseg")
+    if params.get("stackfile") is not None:
+        cargs.extend([
+            "--stack",
+            params.get("stackfile")
+        ])
+    if params.get("gmfile") is not None:
+        cargs.extend([
+            "--gm",
+            params.get("gmfile")
+        ])
+    if params.get("no_fill_csf"):
+        cargs.append("--no-fill-csf")
+    if params.get("dilation") is not None:
+        cargs.extend([
+            "--dil",
+            str(params.get("dilation"))
+        ])
+    if params.get("out_seg") is not None:
+        cargs.extend([
+            "--out-seg",
+            params.get("out_seg")
+        ])
+    if params.get("ttseg") is not None:
+        cargs.extend([
+            "--ttseg",
+            params.get("ttseg")
+        ])
+    if params.get("ttseg_ctab") is not None:
+        cargs.extend([
+            "--ttseg-ctab",
+            params.get("ttseg_ctab")
+        ])
+    if params.get("mgz_format"):
+        cargs.append("--mgz")
+    if params.get("mgh_format"):
+        cargs.append("--mgh")
+    if params.get("nii_format"):
+        cargs.append("--nii")
+    if params.get("nii_gz_format"):
+        cargs.append("--nii.gz")
+    if params.get("ttype_head"):
+        cargs.append("--ttype+head")
+    if params.get("vg_thresh") is not None:
+        cargs.extend([
+            "--vg-thresh",
+            str(params.get("vg_thresh"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    return cargs
+
+
+def mri_compute_volume_fractions_outputs(
+    params: MriComputeVolumeFractionsParameters,
+    execution: Execution,
+) -> MriComputeVolumeFractionsOutputs:
+    """
+    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 = MriComputeVolumeFractionsOutputs(
+        root=execution.output_file("."),
+        output_cortex=execution.output_file(params.get("output_stem") + ".cortex.mgz"),
+        output_subcort_gm=execution.output_file(params.get("output_stem") + ".subcort_gm.mgz"),
+        output_wm=execution.output_file(params.get("output_stem") + ".wm.mgz"),
+        output_csf=execution.output_file(params.get("output_stem") + ".csf.mgz"),
+    )
+    return ret
+
+
+def mri_compute_volume_fractions_execute(
+    params: MriComputeVolumeFractionsParameters,
+    execution: Execution,
+) -> MriComputeVolumeFractionsOutputs:
+    """
+    Computes partial volume fractions for cortex, subcortical GM, WM and CSF.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeVolumeFractionsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_compute_volume_fractions_cargs(params, execution)
+    ret = mri_compute_volume_fractions_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_compute_volume_fractions(
+    output_stem: str,
+    registration_file: InputPathType | None = None,
+    regheader: str | None = None,
+    usf: float | None = None,
+    resolution: float | None = None,
+    resmm: float | None = None,
+    segmentation_file: InputPathType | None = None,
+    wsurf: str | None = None,
+    psurf: str | None = None,
+    no_aseg: bool = False,
+    stackfile: str | None = None,
+    gmfile: str | None = None,
+    no_fill_csf: bool = False,
+    dilation: float | None = None,
+    out_seg: str | None = None,
+    ttseg: str | None = None,
+    ttseg_ctab: str | None = None,
+    mgz_format: bool = False,
+    mgh_format: bool = False,
+    nii_format: bool = False,
+    nii_gz_format: bool = False,
+    ttype_head: bool = False,
+    vg_thresh: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    runner: Runner | None = None,
+) -> MriComputeVolumeFractionsOutputs:
+    """
+    Computes partial volume fractions for cortex, subcortical GM, WM and CSF.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        output_stem: Output stem for generated files (e.g. cortex, subcort_gm,\
+            wm, csf). Files will be saved with this stem in different formats based\
+            on the selected flags.
+        registration_file: Registration file (can be LTA or reg.dat). If using\
+            reg.dat, a template volume is needed.
+        regheader: Specify the subject for regheader.
+        usf: Set anatomical upsample factor (default is 2).
+        resolution: Resolution setting. Sets USF to round(1/res).
+        resmm: Set functional upsampling resolution (default is\
+            aseg->xsize/(USF)).
+        segmentation_file: Use specified segmentation file instead of aseg.mgz.
+        wsurf: Specify the white surface (default is 'white').
+        psurf: Specify the pial surface (default is 'pial').
+        no_aseg: Do not include aseg in processing (useful for testing).
+        stackfile: Put cortex, subcortical GM, WM, CSF into a single\
+            multi-frame file.
+        gmfile: Put cortex + subcortical GM into a single-frame file.
+        no_fill_csf: Do not attempt to fill voxels surrounding segmentation\
+            with extracerebral CSF segmentation.
+        dilation: For xCSF fill, dilate by specified number (default is 3). Use\
+            -1 to fill the entire volume.
+        out_seg: Save segmentation (after adding xCSF voxels).
+        ttseg: Save tissue type segmentation.
+        ttseg_ctab: Save tissue type segmentation color table.
+        mgz_format: Use MGZ format.
+        mgh_format: Use MGH format.
+        nii_format: Use NII format.
+        nii_gz_format: Use NII.GZ format.
+        ttype_head: Use default+head instead of default tissue type info for\
+            segmentation.
+        vg_thresh: Threshold for 'ERROR: LTAconcat(): LTAs 0 and 1 do not\
+            match'.
+        debug: Turn on debugging mode.
+        checkopts: Do not run anything, just check options and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeVolumeFractionsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_VOLUME_FRACTIONS_METADATA)
+    params = mri_compute_volume_fractions_params(
+        output_stem=output_stem,
+        registration_file=registration_file,
+        regheader=regheader,
+        usf=usf,
+        resolution=resolution,
+        resmm=resmm,
+        segmentation_file=segmentation_file,
+        wsurf=wsurf,
+        psurf=psurf,
+        no_aseg=no_aseg,
+        stackfile=stackfile,
+        gmfile=gmfile,
+        no_fill_csf=no_fill_csf,
+        dilation=dilation,
+        out_seg=out_seg,
+        ttseg=ttseg,
+        ttseg_ctab=ttseg_ctab,
+        mgz_format=mgz_format,
+        mgh_format=mgh_format,
+        nii_format=nii_format,
+        nii_gz_format=nii_gz_format,
+        ttype_head=ttype_head,
+        vg_thresh=vg_thresh,
+        debug=debug,
+        checkopts=checkopts,
+    )
+    return mri_compute_volume_fractions_execute(params, execution)
+
+
+__all__ = [
+    "MRI_COMPUTE_VOLUME_FRACTIONS_METADATA",
+    "MriComputeVolumeFractionsOutputs",
+    "MriComputeVolumeFractionsParameters",
+    "mri_compute_volume_fractions",
+    "mri_compute_volume_fractions_params",
+]

niwrap_freesurfer/freesurfer/mri_compute_volume_intensities.py

@@ -0,0 +1,194 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_COMPUTE_VOLUME_INTENSITIES_METADATA = Metadata(
+    id="45ae774d2336d807239cb10e6ca5a797474fe7bd.boutiques",
+    name="mri_compute_volume_intensities",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriComputeVolumeIntensitiesParameters = typing.TypedDict('MriComputeVolumeIntensitiesParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_compute_volume_intensities"],
+    "input_intensity": InputPathType,
+    "volume_fraction_stem": str,
+    "output_volume": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_compute_volume_intensities": mri_compute_volume_intensities_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_compute_volume_intensities": mri_compute_volume_intensities_outputs,
+    }.get(t)
+
+
+class MriComputeVolumeIntensitiesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_compute_volume_intensities(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume_file: OutputPathType
+    """Computed output volume file"""
+
+
+def mri_compute_volume_intensities_params(
+    input_intensity: InputPathType,
+    volume_fraction_stem: str,
+    output_volume: str,
+) -> MriComputeVolumeIntensitiesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_intensity: Input intensity volume.
+        volume_fraction_stem: Volume fraction stem.
+        output_volume: Output volume file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_compute_volume_intensities",
+        "input_intensity": input_intensity,
+        "volume_fraction_stem": volume_fraction_stem,
+        "output_volume": output_volume,
+    }
+    return params
+
+
+def mri_compute_volume_intensities_cargs(
+    params: MriComputeVolumeIntensitiesParameters,
+    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_compute_volume_intensities")
+    cargs.append(execution.input_file(params.get("input_intensity")))
+    cargs.append(params.get("volume_fraction_stem"))
+    cargs.append(params.get("output_volume"))
+    return cargs
+
+
+def mri_compute_volume_intensities_outputs(
+    params: MriComputeVolumeIntensitiesParameters,
+    execution: Execution,
+) -> MriComputeVolumeIntensitiesOutputs:
+    """
+    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 = MriComputeVolumeIntensitiesOutputs(
+        root=execution.output_file("."),
+        output_volume_file=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mri_compute_volume_intensities_execute(
+    params: MriComputeVolumeIntensitiesParameters,
+    execution: Execution,
+) -> MriComputeVolumeIntensitiesOutputs:
+    """
+    A tool to compute volume intensities for a given input intensity volume and
+    volume fraction stem.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeVolumeIntensitiesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_compute_volume_intensities_cargs(params, execution)
+    ret = mri_compute_volume_intensities_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_compute_volume_intensities(
+    input_intensity: InputPathType,
+    volume_fraction_stem: str,
+    output_volume: str,
+    runner: Runner | None = None,
+) -> MriComputeVolumeIntensitiesOutputs:
+    """
+    A tool to compute volume intensities for a given input intensity volume and
+    volume fraction stem.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_intensity: Input intensity volume.
+        volume_fraction_stem: Volume fraction stem.
+        output_volume: Output volume file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeVolumeIntensitiesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_VOLUME_INTENSITIES_METADATA)
+    params = mri_compute_volume_intensities_params(
+        input_intensity=input_intensity,
+        volume_fraction_stem=volume_fraction_stem,
+        output_volume=output_volume,
+    )
+    return mri_compute_volume_intensities_execute(params, execution)
+
+
+__all__ = [
+    "MRI_COMPUTE_VOLUME_INTENSITIES_METADATA",
+    "MriComputeVolumeIntensitiesOutputs",
+    "MriComputeVolumeIntensitiesParameters",
+    "mri_compute_volume_intensities",
+    "mri_compute_volume_intensities_params",
+]