How to use the visualqc.config.default_mri_name function in VisualQC

in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
                        default=default_user_dir,
                        required=False, help=help_text_user_dir)

    in_out.add_argument("-o", "--out_dir", action="store", dest="out_dir",
                        required=False, help=help_text_out_dir,
                        default=None)

    data_source = parser.add_argument_group('Sources of data', ' ')
    data_source.add_argument("-l", "--labels", action="store", dest="labels",
                             default=default_label_set, required=False, nargs='+',
                             help=help_text_label, metavar='label')

    data_source.add_argument("-m", "--mri_name", action="store", dest="mri_name",
                             default=default_mri_name, required=False,
                             help=help_text_mri_name)

    data_source.add_argument("-g", "--seg_name", action="store", dest="seg_name",
                             default=default_seg_name, required=False,
                             help=help_text_seg_name)

    vis_args = parser.add_argument_group('Overlay options', ' ')
    vis_args.add_argument("-v", "--vis_type", action="store", dest="vis_type",
                          choices=visualization_combination_choices,
                          default=default_vis_type, required=False,
                          help=help_text_vis_type)

    vis_args.add_argument("-c", "--contour_color", action="store", dest="contour_color",
                          default=cfg.default_contour_face_color, required=False,
                          help=help_text_contour_color)

.. parsed-literal::

        sub001
        sub002
        cn_003
        cn_004

    \n""")

    help_text_mri_name = textwrap.dedent("""
    Specifies the name of MRI image to serve as the reference slice.
    Typical options include orig.mgz, brainmask.mgz, T1.mgz etc.
    Make sure to choose the right vis_type.

    Default: {} (within the mri folder of Freesurfer format).
    \n""".format(cfg.default_mri_name))

    help_text_seg_name = textwrap.dedent("""
    Specifies the name of segmentation image (volumetric) to be overlaid on the MRI.
    Typical options include aparc+aseg.mgz, aseg.mgz, wmparc.mgz. 
    Make sure to choose the right vis_type. 

    Default: {} (within the mri folder of Freesurfer format).
    \n""".format(cfg.default_seg_name))

    help_text_out_dir = textwrap.dedent("""
    Output folder to store the visualizations & ratings.
    Default: a new folder called ``{}`` will be created inside the ``fs_dir``
    \n""".format(cfg.default_out_dir_name))

    help_text_vis_type = textwrap.dedent("""
    Specifies the type of visualizations/overlay requested.

in_out = parser.add_argument_group('Input and output', ' ')

    in_out.add_argument("-i", "--id_list", action="store", dest="id_list",
                        default=None, required=False, help=help_text_id_list)

    in_out.add_argument("-f", "--fs_dir", action="store", dest="fs_dir",
                        default=cfg.default_freesurfer_dir,
                        required=False, help=help_text_fs_dir)

    in_out.add_argument("-o", "--out_dir", action="store", dest="out_dir",
                        required=False, help=help_text_out_dir,
                        default=None)

    in_out.add_argument("-m", "--mri_name", action="store", dest="mri_name",
                        default=cfg.default_mri_name, required=False,
                        help=help_text_mri_name)

    in_out.add_argument("-g", "--seg_name", action="store", dest="seg_name",
                        default=cfg.default_seg_name, required=False,
                        help=help_text_seg_name)

    in_out.add_argument("-l", "--labels", action="store", dest="label_set",
                        default=cfg.default_label_set,
                        nargs='+', metavar='label',
                        required=False, help=help_text_label)

    vis_args = parser.add_argument_group('Overlay options', ' ')
    vis_args.add_argument("-v", "--vis_type", action="store", dest="vis_type",
                          choices=cfg.visualization_combination_choices,
                          default=cfg.default_vis_type, required=False,
                          help=help_text_vis_type)

Output folder to store the visualizations & ratings.
    Default: a new folder called ``{}`` will be created inside the ``fs_dir``
    \n""".format(cfg.default_out_dir_name))

    in_out = parser.add_argument_group('Input and output', ' ')

    in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
                        default=cfg.default_user_dir,
                        required=False, help=help_text_user_dir)

    in_out.add_argument("-d", "--defaced_name", action="store", dest="defaced_name",
                        default=cfg.default_defaced_mri_name, required=False,
                        help=help_text_defaced_mri_name)

    in_out.add_argument("-m", "--mri_name", action="store", dest="mri_name",
                        default=cfg.default_mri_name, required=False,
                        help=help_text_mri_name)

    in_out.add_argument("-r", "--render_name", action="store", dest="render_name",
                        default=cfg.default_render_name, required=False,
                        help=help_text_render_name)

    in_out.add_argument("-o", "--out_dir", action="store", dest="out_dir",
                        required=False, help=help_text_out_dir,
                        default=None)

    in_out.add_argument("-i", "--id_list", action="store", dest="id_list",
                        default=None, required=False, help=help_text_id_list)

    return parser

cn_004

    \n""")

    help_text_defaced_mri_name = textwrap.dedent("""
    Specifies the name of defaced MRI image to be rated.

    Default: {}
    \n""".format(cfg.default_defaced_mri_name))

    help_text_mri_name = textwrap.dedent("""
    Specifies the name of MRI image that is NOT defaced, to check the accuracy of
    the defacing algorithm.

    Default: {}
    \n""".format(cfg.default_mri_name))

    help_text_render_name = textwrap.dedent("""
    Specifies the name of 3D render of the MRI scan.

    Default: {}
    \n""".format(cfg.default_render_name))

    help_text_out_dir = textwrap.dedent("""
    Output folder to store the visualizations & ratings.
    Default: a new folder called ``{}`` will be created inside the ``fs_dir``
    \n""".format(cfg.default_out_dir_name))

    in_out = parser.add_argument_group('Input and output', ' ')

    in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
                        default=cfg.default_user_dir,

def __init__(self,
                 id_list,
                 images_for_id,
                 in_dir,
                 out_dir,
                 vis_type=cfg.default_vis_type,
                 label_set=cfg.default_label_set,
                 issue_list=cfg.default_rating_list,
                 mri_name=cfg.default_mri_name,
                 seg_name=cfg.default_seg_name,
                 alpha_set=cfg.default_alpha_set,
                 outlier_method=cfg.default_outlier_detection_method,
                 outlier_fraction=cfg.default_outlier_fraction,
                 outlier_feat_types=cfg.freesurfer_features_outlier_detection,
                 source_of_features=cfg.default_source_of_features_freesurfer,
                 disable_outlier_detection=False,
                 no_surface_vis=False,
                 views=cfg.default_views,
                 num_slices_per_view=cfg.default_num_slices,
                 num_rows_per_view=cfg.default_num_rows):
        """Constructor"""

        super().__init__(id_list, in_dir, out_dir,
                         outlier_method, outlier_fraction,
                         outlier_feat_types, disable_outlier_detection)

Default: {} {}.  Play with these values to find something that works for you and the dataset.
    \n""".format(default_alpha_mri, default_alpha_seg))

    help_text_label = textwrap.dedent("""
    Specifies the set of labels to include for overlay.
    
    Default: None (show all the labels in the selected segmentation)
    \n""")

    help_text_mri_name = textwrap.dedent("""
    Specifies the name of MRI image to serve as the reference slice.
    Typical options include orig.mgz, brainmask.mgz, T1.mgz etc.
    Make sure to choose the right vis_type.
    
    Default: {} (within the mri folder of Freesurfer format).
    \n""".format(default_mri_name))

    help_text_seg_name = textwrap.dedent("""
    Specifies the name of segmentation image (volumetric) to be overlaid on the MRI.
    Typical options include aparc+aseg.mgz, aseg.mgz, wmparc.mgz. 
    Make sure to choose the right vis_type. 

    Default: {} (within the mri folder of Freesurfer format).
    \n""".format(default_seg_name))

    help_text_views = textwrap.dedent("""
    Specifies the set of views to display - could be just 1 view, or 2 or all 3.
    Example: --views 0 (typically sagittal) or --views 1 2 (axial and coronal)
    Default: {} {} {} (show all the views in the selected segmentation)
    \n""".format(default_views[0], default_views[1], default_views[2]))

    help_text_num_slices = textwrap.dedent("""