niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_proc_convert_dcm_dwis.py

@@ -0,0 +1,374 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_CONVERT_DCM_DWIS_METADATA = Metadata(
+    id="9b9610517874019289f1b6f2dec8529be62fcd51.boutiques",
+    name="fat_proc_convert_dcm_dwis",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcConvertDcmDwisParameters = typing.TypedDict('FatProcConvertDcmDwisParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_convert_dcm_dwis"],
+    "dicom_dir": str,
+    "output_prefix": str,
+    "nifti_files": typing.NotRequired[list[InputPathType] | None],
+    "bvec_files": typing.NotRequired[list[InputPathType] | None],
+    "bval_files": typing.NotRequired[list[InputPathType] | None],
+    "work_dir": typing.NotRequired[str | None],
+    "orientation": typing.NotRequired[str | None],
+    "origin_xyz": typing.NotRequired[list[float] | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "no_flip": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "reorient_off": bool,
+    "no_clean": bool,
+    "no_cmd_out": bool,
+    "no_qc_view": bool,
+    "do_movie": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_proc_convert_dcm_dwis": fat_proc_convert_dcm_dwis_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 {
+        "fat_proc_convert_dcm_dwis": fat_proc_convert_dcm_dwis_outputs,
+    }.get(t)
+
+
+class FatProcConvertDcmDwisOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_convert_dcm_dwis(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_nifti: OutputPathType
+    """A NIFTI file with N volumes."""
+    output_rvec: OutputPathType
+    """A row-wise (3xN) bvec file of the (unit-magnitude) gradient
+    orientations."""
+    output_bval: OutputPathType
+    """A row-wise (1xN) bval file of the gradient magnitudes."""
+    output_mat_a: OutputPathType
+    """A column-wise (Nx6) AFNI-style matrix file of the (scaled) b-matrix
+    values."""
+    output_mat_t: OutputPathType
+    """A column-wise (Nx6) TORTOISE-style matrix file of the (scaled) b-matrix
+    values."""
+    output_cvec: OutputPathType
+    """A column-wise (Nx3) bvec file of the (b-magn scaled) gradient
+    orientations."""
+
+
+def fat_proc_convert_dcm_dwis_params(
+    dicom_dir: str,
+    output_prefix: str,
+    nifti_files: list[InputPathType] | None = None,
+    bvec_files: list[InputPathType] | None = None,
+    bval_files: list[InputPathType] | None = None,
+    work_dir: str | None = None,
+    orientation: str | None = None,
+    origin_xyz: list[float] | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    qc_prefix: str | None = None,
+    reorient_off: bool = False,
+    no_clean: bool = False,
+    no_cmd_out: bool = False,
+    no_qc_view: bool = False,
+    do_movie: str | None = None,
+) -> FatProcConvertDcmDwisParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dicom_dir: Directory of DICOM files of the DWI data with 'AP' phase\
+            encoding. Can contain a wildcard expression for several directories.
+        output_prefix: Prefix (and path) for output data (e.g., *.nii.gz,\
+            *.bvec, *.bval files). Required.
+        nifti_files: One or more NIFTI files of DWIs.
+        bvec_files: One or more row-wise, gradient (unit-magnitude) files\
+            (e.g., *.bvec).
+        bval_files: One or more bvalue files (e.g., *.bval).
+        work_dir: Optional working directory for intermediate files.
+        orientation: Optional chance to reset orientation of the volume files\
+            (default is currently 'RAI').
+        origin_xyz: Explicit origin coordinates (X, Y, Z).
+        flip_x: Flip gradients along the X-axis.
+        flip_y: Flip gradients along the Y-axis.
+        flip_z: Flip gradients along the Z-axis.
+        no_flip: Prevent flipping of gradients (default).
+        qc_prefix: Set the prefix for QC image files separately (default is\
+            '').
+        reorient_off: Turn off reorigin calculation and reorientation.
+        no_clean: Do not remove the working directory of intermediate files\
+            (default is to delete it).
+        no_cmd_out: Do not save the command line call and location where it was\
+            run.
+        no_qc_view: Do not generate QC image files.
+        do_movie: Generate a movie of the newly created dataset (AGIF or MPEG).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_convert_dcm_dwis",
+        "dicom_dir": dicom_dir,
+        "output_prefix": output_prefix,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+        "no_flip": no_flip,
+        "reorient_off": reorient_off,
+        "no_clean": no_clean,
+        "no_cmd_out": no_cmd_out,
+        "no_qc_view": no_qc_view,
+    }
+    if nifti_files is not None:
+        params["nifti_files"] = nifti_files
+    if bvec_files is not None:
+        params["bvec_files"] = bvec_files
+    if bval_files is not None:
+        params["bval_files"] = bval_files
+    if work_dir is not None:
+        params["work_dir"] = work_dir
+    if orientation is not None:
+        params["orientation"] = orientation
+    if origin_xyz is not None:
+        params["origin_xyz"] = origin_xyz
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    if do_movie is not None:
+        params["do_movie"] = do_movie
+    return params
+
+
+def fat_proc_convert_dcm_dwis_cargs(
+    params: FatProcConvertDcmDwisParameters,
+    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("fat_proc_convert_dcm_dwis")
+    cargs.append(params.get("dicom_dir"))
+    cargs.append(params.get("output_prefix"))
+    if params.get("nifti_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("nifti_files")])
+    if params.get("bvec_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("bvec_files")])
+    if params.get("bval_files") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("bval_files")])
+    if params.get("work_dir") is not None:
+        cargs.append(params.get("work_dir"))
+    if params.get("orientation") is not None:
+        cargs.append(params.get("orientation"))
+    if params.get("origin_xyz") is not None:
+        cargs.extend(map(str, params.get("origin_xyz")))
+    if params.get("flip_x"):
+        cargs.append("-flip_x")
+    if params.get("flip_y"):
+        cargs.append("-flip_y")
+    if params.get("flip_z"):
+        cargs.append("-flip_z")
+    if params.get("no_flip"):
+        cargs.append("-no_flip")
+    if params.get("qc_prefix") is not None:
+        cargs.append(params.get("qc_prefix"))
+    if params.get("reorient_off"):
+        cargs.append("-reorig_reorient_off")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("no_cmd_out"):
+        cargs.append("-no_cmd_out")
+    if params.get("no_qc_view"):
+        cargs.append("-no_qc_view")
+    if params.get("do_movie") is not None:
+        cargs.extend([
+            "-do_movie",
+            params.get("do_movie")
+        ])
+    return cargs
+
+
+def fat_proc_convert_dcm_dwis_outputs(
+    params: FatProcConvertDcmDwisParameters,
+    execution: Execution,
+) -> FatProcConvertDcmDwisOutputs:
+    """
+    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 = FatProcConvertDcmDwisOutputs(
+        root=execution.output_file("."),
+        output_nifti=execution.output_file(params.get("output_prefix") + ".nii.gz"),
+        output_rvec=execution.output_file(params.get("output_prefix") + ".rvec"),
+        output_bval=execution.output_file(params.get("output_prefix") + ".bval"),
+        output_mat_a=execution.output_file(params.get("output_prefix") + "_matA.dat"),
+        output_mat_t=execution.output_file(params.get("output_prefix") + "_matT.dat"),
+        output_cvec=execution.output_file(params.get("output_prefix") + "_cvec.dat"),
+    )
+    return ret
+
+
+def fat_proc_convert_dcm_dwis_execute(
+    params: FatProcConvertDcmDwisParameters,
+    execution: Execution,
+) -> FatProcConvertDcmDwisOutputs:
+    """
+    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format, reorient
+    volumetric data, and glue together multiple sessions/directories of data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcConvertDcmDwisOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_convert_dcm_dwis_cargs(params, execution)
+    ret = fat_proc_convert_dcm_dwis_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_convert_dcm_dwis(
+    dicom_dir: str,
+    output_prefix: str,
+    nifti_files: list[InputPathType] | None = None,
+    bvec_files: list[InputPathType] | None = None,
+    bval_files: list[InputPathType] | None = None,
+    work_dir: str | None = None,
+    orientation: str | None = None,
+    origin_xyz: list[float] | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    qc_prefix: str | None = None,
+    reorient_off: bool = False,
+    no_clean: bool = False,
+    no_cmd_out: bool = False,
+    no_qc_view: bool = False,
+    do_movie: str | None = None,
+    runner: Runner | None = None,
+) -> FatProcConvertDcmDwisOutputs:
+    """
+    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format, reorient
+    volumetric data, and glue together multiple sessions/directories of data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dicom_dir: Directory of DICOM files of the DWI data with 'AP' phase\
+            encoding. Can contain a wildcard expression for several directories.
+        output_prefix: Prefix (and path) for output data (e.g., *.nii.gz,\
+            *.bvec, *.bval files). Required.
+        nifti_files: One or more NIFTI files of DWIs.
+        bvec_files: One or more row-wise, gradient (unit-magnitude) files\
+            (e.g., *.bvec).
+        bval_files: One or more bvalue files (e.g., *.bval).
+        work_dir: Optional working directory for intermediate files.
+        orientation: Optional chance to reset orientation of the volume files\
+            (default is currently 'RAI').
+        origin_xyz: Explicit origin coordinates (X, Y, Z).
+        flip_x: Flip gradients along the X-axis.
+        flip_y: Flip gradients along the Y-axis.
+        flip_z: Flip gradients along the Z-axis.
+        no_flip: Prevent flipping of gradients (default).
+        qc_prefix: Set the prefix for QC image files separately (default is\
+            '').
+        reorient_off: Turn off reorigin calculation and reorientation.
+        no_clean: Do not remove the working directory of intermediate files\
+            (default is to delete it).
+        no_cmd_out: Do not save the command line call and location where it was\
+            run.
+        no_qc_view: Do not generate QC image files.
+        do_movie: Generate a movie of the newly created dataset (AGIF or MPEG).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcConvertDcmDwisOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_CONVERT_DCM_DWIS_METADATA)
+    params = fat_proc_convert_dcm_dwis_params(
+        dicom_dir=dicom_dir,
+        output_prefix=output_prefix,
+        nifti_files=nifti_files,
+        bvec_files=bvec_files,
+        bval_files=bval_files,
+        work_dir=work_dir,
+        orientation=orientation,
+        origin_xyz=origin_xyz,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+        no_flip=no_flip,
+        qc_prefix=qc_prefix,
+        reorient_off=reorient_off,
+        no_clean=no_clean,
+        no_cmd_out=no_cmd_out,
+        no_qc_view=no_qc_view,
+        do_movie=do_movie,
+    )
+    return fat_proc_convert_dcm_dwis_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_CONVERT_DCM_DWIS_METADATA",
+    "FatProcConvertDcmDwisOutputs",
+    "FatProcConvertDcmDwisParameters",
+    "fat_proc_convert_dcm_dwis",
+    "fat_proc_convert_dcm_dwis_params",
+]

niwrap_afni/afni/fat_proc_decmap.py

@@ -0,0 +1,321 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_DECMAP_METADATA = Metadata(
+    id="a736dc72fa9ccb8800e84305855b09096c833b1d.boutiques",
+    name="fat_proc_decmap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcDecmapParameters = typing.TypedDict('FatProcDecmapParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_decmap"],
+    "in_fa": InputPathType,
+    "in_v1": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "fa_thr": typing.NotRequired[float | None],
+    "fa_sca": typing.NotRequired[float | None],
+    "workdir": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+    "no_qc_view": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_proc_decmap": fat_proc_decmap_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 {
+        "fat_proc_decmap": fat_proc_decmap_outputs,
+    }.get(t)
+
+
+class FatProcDecmapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_decmap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_dec_rgb: OutputPathType
+    """Single file of type 'rgb' for RGB coloration display."""
+    outfile_dec_unwt_thr: OutputPathType
+    """Single file of type 'rgb' without FA weighting but using FA to threshold
+    where DEC values are calculated."""
+    outfile_dec_sca: OutputPathType
+    """DEC file additionally scaled by a value (such as 0.7)."""
+    qc_dec_images: OutputPathType
+    """Set of cor, axi, and sag images (each a 5x3 montage) of the DEC data."""
+    qc_dec_unwt_thrx_images: OutputPathType
+    """Set of cor, axi, and sag images (each a 5x3 montage) of the DEC
+    unweighted thresholded data."""
+    qc_dec_sca_images: OutputPathType
+    """Set of cor, axi, and sag images (each a 5x3 montage) of the DEC scaled
+    data."""
+
+
+def fat_proc_decmap_params(
+    in_fa: InputPathType,
+    in_v1: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    fa_thr: float | None = None,
+    fa_sca: float | None = None,
+    workdir: str | None = None,
+    no_clean: bool = False,
+    qc_prefix: str | None = None,
+    no_cmd_out: bool = False,
+    no_qc_view: bool = False,
+) -> FatProcDecmapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_fa: Input FA (scalar) map.
+        in_v1: Input first eigenvector (3-vector) map.
+        prefix: Set prefix (and path) for output DWI data.
+        mask: Optional mask for picking out a region. Otherwise, only places\
+            with FA>0 are given coloration.
+        fa_thr: For QC1 type of DEC images, use FFF to threshold where DEC\
+            values are calculated (default: 0.2).
+        fa_sca: For QC2 type of DEC images, use SSS to scale the FA weighting\
+            of what would otherwise be a 'classical' DEC map (default: 0.7).
+        workdir: Specify a working directory, which can be removed (default:\
+            '__WORKING_decmap').
+        no_clean: Do not delete temporary files when finishing.
+        qc_prefix: Set the prefix of the QC image files (default: 'PREFIX').
+        no_cmd_out: Do not save the command line call of this program and\
+            location where it was run.
+        no_qc_view: Turn off generating QC image files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_decmap",
+        "in_fa": in_fa,
+        "in_v1": in_v1,
+        "prefix": prefix,
+        "no_clean": no_clean,
+        "no_cmd_out": no_cmd_out,
+        "no_qc_view": no_qc_view,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if fa_thr is not None:
+        params["fa_thr"] = fa_thr
+    if fa_sca is not None:
+        params["fa_sca"] = fa_sca
+    if workdir is not None:
+        params["workdir"] = workdir
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    return params
+
+
+def fat_proc_decmap_cargs(
+    params: FatProcDecmapParameters,
+    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("fat_proc_decmap")
+    cargs.extend([
+        "-in_fa",
+        execution.input_file(params.get("in_fa"))
+    ])
+    cargs.extend([
+        "-in_v1",
+        execution.input_file(params.get("in_v1"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("fa_thr") is not None:
+        cargs.extend([
+            "-fa_thr",
+            str(params.get("fa_thr"))
+        ])
+    if params.get("fa_sca") is not None:
+        cargs.extend([
+            "-fa_sca",
+            str(params.get("fa_sca"))
+        ])
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("qc_prefix") is not None:
+        cargs.extend([
+            "-qc_prefix",
+            params.get("qc_prefix")
+        ])
+    if params.get("no_cmd_out"):
+        cargs.append("-no_cmd_out")
+    if params.get("no_qc_view"):
+        cargs.append("-no_qc_view")
+    return cargs
+
+
+def fat_proc_decmap_outputs(
+    params: FatProcDecmapParameters,
+    execution: Execution,
+) -> FatProcDecmapOutputs:
+    """
+    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 = FatProcDecmapOutputs(
+        root=execution.output_file("."),
+        outfile_dec_rgb=execution.output_file(params.get("prefix") + "_dec.nii.gz"),
+        outfile_dec_unwt_thr=execution.output_file(params.get("prefix") + "_dec_unwt_thr.nii.gz"),
+        outfile_dec_sca=execution.output_file(params.get("prefix") + "_dec_sca*.nii.gz"),
+        qc_dec_images=execution.output_file(params.get("prefix") + "_qc_dec*.png"),
+        qc_dec_unwt_thrx_images=execution.output_file(params.get("prefix") + "_qc_dec_unwt_thrx*.png"),
+        qc_dec_sca_images=execution.output_file(params.get("prefix") + "_qc_dec_sca*.png"),
+    )
+    return ret
+
+
+def fat_proc_decmap_execute(
+    params: FatProcDecmapParameters,
+    execution: Execution,
+) -> FatProcDecmapOutputs:
+    """
+    This program makes a directionally encoded color (DEC) map for DTI results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcDecmapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_decmap_cargs(params, execution)
+    ret = fat_proc_decmap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_decmap(
+    in_fa: InputPathType,
+    in_v1: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    fa_thr: float | None = None,
+    fa_sca: float | None = None,
+    workdir: str | None = None,
+    no_clean: bool = False,
+    qc_prefix: str | None = None,
+    no_cmd_out: bool = False,
+    no_qc_view: bool = False,
+    runner: Runner | None = None,
+) -> FatProcDecmapOutputs:
+    """
+    This program makes a directionally encoded color (DEC) map for DTI results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_fa: Input FA (scalar) map.
+        in_v1: Input first eigenvector (3-vector) map.
+        prefix: Set prefix (and path) for output DWI data.
+        mask: Optional mask for picking out a region. Otherwise, only places\
+            with FA>0 are given coloration.
+        fa_thr: For QC1 type of DEC images, use FFF to threshold where DEC\
+            values are calculated (default: 0.2).
+        fa_sca: For QC2 type of DEC images, use SSS to scale the FA weighting\
+            of what would otherwise be a 'classical' DEC map (default: 0.7).
+        workdir: Specify a working directory, which can be removed (default:\
+            '__WORKING_decmap').
+        no_clean: Do not delete temporary files when finishing.
+        qc_prefix: Set the prefix of the QC image files (default: 'PREFIX').
+        no_cmd_out: Do not save the command line call of this program and\
+            location where it was run.
+        no_qc_view: Turn off generating QC image files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcDecmapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_DECMAP_METADATA)
+    params = fat_proc_decmap_params(
+        in_fa=in_fa,
+        in_v1=in_v1,
+        prefix=prefix,
+        mask=mask,
+        fa_thr=fa_thr,
+        fa_sca=fa_sca,
+        workdir=workdir,
+        no_clean=no_clean,
+        qc_prefix=qc_prefix,
+        no_cmd_out=no_cmd_out,
+        no_qc_view=no_qc_view,
+    )
+    return fat_proc_decmap_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_DECMAP_METADATA",
+    "FatProcDecmapOutputs",
+    "FatProcDecmapParameters",
+    "fat_proc_decmap",
+    "fat_proc_decmap_params",
+]