niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/adjunct_suma_fs_mask_and_qc.py

@@ -0,0 +1,249 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA = Metadata(
+    id="e333368d139aab06ce173382ee2a0cb69f091a99.boutiques",
+    name="adjunct_suma_fs_mask_and_qc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctSumaFsMaskAndQcParameters = typing.TypedDict('AdjunctSumaFsMaskAndQcParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_suma_fs_mask_and_qc"],
+    "subj_id": str,
+    "suma_dir": str,
+    "no_clean": bool,
+    "help": bool,
+    "hview": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_suma_fs_mask_and_qc": adjunct_suma_fs_mask_and_qc_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 {
+        "adjunct_suma_fs_mask_and_qc": adjunct_suma_fs_mask_and_qc_outputs,
+    }.get(t)
+
+
+class AdjunctSumaFsMaskAndQcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_suma_fs_mask_and_qc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fs_parc_wb_mask: OutputPathType
+    """Whole brain mask based on the FS parcellation created by this script."""
+    qc_image_00: OutputPathType
+    """QC image with overlay of brainmask.nii* volume in red and parcellated
+    subset in black."""
+    qc_image_01: OutputPathType
+    """QC image with overlay of fs_parc_wb_mask.nii.gz."""
+    qc_image_02: OutputPathType
+    """QC image with overlay of tissue segmentations."""
+    qc_image_03: OutputPathType
+    """QC image with overlay of GM."""
+    qc_image_04: OutputPathType
+    """QC image with overlay of WM."""
+    qc_image_05: OutputPathType
+    """QC image with overlay of "2000" atlas parcellation."""
+
+
+def adjunct_suma_fs_mask_and_qc_params(
+    subj_id: str,
+    suma_dir: str,
+    no_clean: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+    version: bool = False,
+) -> AdjunctSumaFsMaskAndQcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subj_id: Subject ID.
+        suma_dir: SUMA/ directory output by AFNI's @SUMA_Make_Spec_FS.
+        no_clean: Do not remove temporary working subdirectory (default: remove\
+            it).
+        help_: Show help.
+        hview: Show help in text editor.
+        version: Show version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_suma_fs_mask_and_qc",
+        "subj_id": subj_id,
+        "suma_dir": suma_dir,
+        "no_clean": no_clean,
+        "help": help_,
+        "hview": hview,
+        "version": version,
+    }
+    return params
+
+
+def adjunct_suma_fs_mask_and_qc_cargs(
+    params: AdjunctSumaFsMaskAndQcParameters,
+    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("adjunct_suma_fs_mask_and_qc")
+    cargs.extend([
+        "-sid",
+        params.get("subj_id")
+    ])
+    cargs.extend([
+        "-suma_dir",
+        params.get("suma_dir")
+    ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hview"):
+        cargs.append("-hview")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def adjunct_suma_fs_mask_and_qc_outputs(
+    params: AdjunctSumaFsMaskAndQcParameters,
+    execution: Execution,
+) -> AdjunctSumaFsMaskAndQcOutputs:
+    """
+    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 = AdjunctSumaFsMaskAndQcOutputs(
+        root=execution.output_file("."),
+        fs_parc_wb_mask=execution.output_file("SUMA/fs_parc_wb_mask.nii.gz"),
+        qc_image_00=execution.output_file("SUMA/qc_00*.jpg"),
+        qc_image_01=execution.output_file("SUMA/qc_01*.jpg"),
+        qc_image_02=execution.output_file("SUMA/qc_02*.jpg"),
+        qc_image_03=execution.output_file("SUMA/qc_03*.jpg"),
+        qc_image_04=execution.output_file("SUMA/qc_04*.jpg"),
+        qc_image_05=execution.output_file("SUMA/qc_05*.jpg"),
+    )
+    return ret
+
+
+def adjunct_suma_fs_mask_and_qc_execute(
+    params: AdjunctSumaFsMaskAndQcParameters,
+    execution: Execution,
+) -> AdjunctSumaFsMaskAndQcOutputs:
+    """
+    Script for quickly making some QC images for the SUMA/ directory created by
+    @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSumaFsMaskAndQcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_suma_fs_mask_and_qc_cargs(params, execution)
+    ret = adjunct_suma_fs_mask_and_qc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_suma_fs_mask_and_qc(
+    subj_id: str,
+    suma_dir: str,
+    no_clean: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> AdjunctSumaFsMaskAndQcOutputs:
+    """
+    Script for quickly making some QC images for the SUMA/ directory created by
+    @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        subj_id: Subject ID.
+        suma_dir: SUMA/ directory output by AFNI's @SUMA_Make_Spec_FS.
+        no_clean: Do not remove temporary working subdirectory (default: remove\
+            it).
+        help_: Show help.
+        hview: Show help in text editor.
+        version: Show version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSumaFsMaskAndQcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA)
+    params = adjunct_suma_fs_mask_and_qc_params(
+        subj_id=subj_id,
+        suma_dir=suma_dir,
+        no_clean=no_clean,
+        help_=help_,
+        hview=hview,
+        version=version,
+    )
+    return adjunct_suma_fs_mask_and_qc_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA",
+    "AdjunctSumaFsMaskAndQcOutputs",
+    "AdjunctSumaFsMaskAndQcParameters",
+    "adjunct_suma_fs_mask_and_qc",
+    "adjunct_suma_fs_mask_and_qc_params",
+]

niwrap_afni/afni/adjunct_suma_fs_roi_info.py

@@ -0,0 +1,228 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_SUMA_FS_ROI_INFO_METADATA = Metadata(
+    id="779dea93198c9c27ce2d88ef43623927b9130d07.boutiques",
+    name="adjunct_suma_fs_roi_info",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctSumaFsRoiInfoParameters = typing.TypedDict('AdjunctSumaFsRoiInfoParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_suma_fs_roi_info"],
+    "subject_id": str,
+    "suma_directory": str,
+    "help": bool,
+    "hview": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_suma_fs_roi_info": adjunct_suma_fs_roi_info_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 {
+        "adjunct_suma_fs_roi_info": adjunct_suma_fs_roi_info_outputs,
+    }.get(t)
+
+
+class AdjunctSumaFsRoiInfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_suma_fs_roi_info(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    rois_2000_ft: OutputPathType
+    """Info for the '2000' parcellation."""
+    rois_2009_ft: OutputPathType
+    """Info for the '2009' parcellation."""
+    segs_2000_ft: OutputPathType
+    """Info for the '2000' parcellation brain mask and tissue/segmentations."""
+    segs_2009_ft: OutputPathType
+    """Info for the '2009' parcellation brain mask and tissue/segmentations."""
+
+
+def adjunct_suma_fs_roi_info_params(
+    subject_id: str,
+    suma_directory: str,
+    help_: bool = False,
+    hview: bool = False,
+    version: bool = False,
+) -> AdjunctSumaFsRoiInfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Subject ID.
+        suma_directory: SUMA directory output by AFNI's @SUMA_Make_Spec_FS.
+        help_: Show help.
+        hview: Show help in text editor.
+        version: Show version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_suma_fs_roi_info",
+        "subject_id": subject_id,
+        "suma_directory": suma_directory,
+        "help": help_,
+        "hview": hview,
+        "version": version,
+    }
+    return params
+
+
+def adjunct_suma_fs_roi_info_cargs(
+    params: AdjunctSumaFsRoiInfoParameters,
+    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("adjunct_suma_fs_roi_info")
+    cargs.extend([
+        "-sid",
+        params.get("subject_id")
+    ])
+    cargs.extend([
+        "-suma_dir",
+        params.get("suma_directory")
+    ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hview"):
+        cargs.append("-hview")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def adjunct_suma_fs_roi_info_outputs(
+    params: AdjunctSumaFsRoiInfoParameters,
+    execution: Execution,
+) -> AdjunctSumaFsRoiInfoOutputs:
+    """
+    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 = AdjunctSumaFsRoiInfoOutputs(
+        root=execution.output_file("."),
+        rois_2000_ft=execution.output_file("stats_fs_rois_2000_FT.1D"),
+        rois_2009_ft=execution.output_file("stats_fs_rois_2009_FT.1D"),
+        segs_2000_ft=execution.output_file("stats_fs_segs_2000_FT.1D"),
+        segs_2009_ft=execution.output_file("stats_fs_segs_2009_FT.1D"),
+    )
+    return ret
+
+
+def adjunct_suma_fs_roi_info_execute(
+    params: AdjunctSumaFsRoiInfoParameters,
+    execution: Execution,
+) -> AdjunctSumaFsRoiInfoOutputs:
+    """
+    Script for making ROI stats for the SUMA/ directory created by
+    @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSumaFsRoiInfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_suma_fs_roi_info_cargs(params, execution)
+    ret = adjunct_suma_fs_roi_info_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_suma_fs_roi_info(
+    subject_id: str,
+    suma_directory: str,
+    help_: bool = False,
+    hview: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> AdjunctSumaFsRoiInfoOutputs:
+    """
+    Script for making ROI stats for the SUMA/ directory created by
+    @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        subject_id: Subject ID.
+        suma_directory: SUMA directory output by AFNI's @SUMA_Make_Spec_FS.
+        help_: Show help.
+        hview: Show help in text editor.
+        version: Show version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSumaFsRoiInfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SUMA_FS_ROI_INFO_METADATA)
+    params = adjunct_suma_fs_roi_info_params(
+        subject_id=subject_id,
+        suma_directory=suma_directory,
+        help_=help_,
+        hview=hview,
+        version=version,
+    )
+    return adjunct_suma_fs_roi_info_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_SUMA_FS_ROI_INFO_METADATA",
+    "AdjunctSumaFsRoiInfoOutputs",
+    "AdjunctSumaFsRoiInfoParameters",
+    "adjunct_suma_fs_roi_info",
+    "adjunct_suma_fs_roi_info_params",
+]