How to use the visualqc.config function in VisualQC

error_msg='defaced mri')
        self.orig_img = read_image(self.images_for_id[unit_id]['original'],
                                   error_msg='T1 mri')

        self.render_img_list = list()
        for rimg_path in self.images_for_id[unit_id]['render']:
            try:
                self.render_img_list.append(imread(rimg_path))
            except:
                raise IOError('Unable to read the 3D rendered image @\n {}'
                              ''.format(rimg_path))

        # crop, trim, and rescale
        self.defaced_img = rescale_without_outliers(
            self.defaced_img, padding=self.padding,
            trim_percentile=cfg.defacing_trim_percentile)
        self.orig_img = rescale_without_outliers(
            self.orig_img, padding=self.padding,
            trim_percentile=cfg.defacing_trim_percentile)
        self.currently_showing = None

        skip_subject = False
        if np.count_nonzero(self.defaced_img) == 0 or \
            np.count_nonzero(self.orig_img) == 0:
            skip_subject = True
            print('Defaced or original MR image is empty!')

        self.slice_picker = SlicePicker(self.orig_img,
                                        view_set=self.collage.view_set,
                                        num_slices=self.collage.num_slices,
                                        sampler=cfg.defacing_slice_locations)

def add_histogram_panel(self):
        """Extra axis for histogram of cortical thickness!"""

        if not self.vis_type in cfg.cortical_types:
            return

        self.ax_hist = plt.axes(cfg.position_histogram_freesurfer)
        self.ax_hist.set(xticks=cfg.xticks_histogram_freesurfer,
                         xticklabels=cfg.xticks_histogram_freesurfer,
                         yticks=[], autoscaley_on=True)
        self.ax_hist.set_prop_cycle('color', cfg.color_histogram_freesurfer)
        self.ax_hist.set_title(cfg.title_histogram_freesurfer, fontsize='small')

def __init__(self,
                 fig,
                 axes,
                 issue_list=cfg.defacing_default_issue_list,
                 next_button_callback=None,
                 quit_button_callback=None,
                 processing_choice_callback=None,
                 map_key_to_callback=None):
        """Constructor"""

        super().__init__(fig, axes, next_button_callback, quit_button_callback)

        self.issue_list = issue_list

        self.prev_axis = None
        self.prev_ax_pos = None
        self.zoomed_in = False
        self.next_button_callback = next_button_callback
        self.quit_button_callback = quit_button_callback
        self.processing_choice_callback = processing_choice_callback

def add_histogram_panel(self):
        """Extra axis for histogram"""

        self.ax_hist = plt.axes(cfg.position_histogram_t1_mri)
        self.ax_hist.set_xticks(cfg.xticks_histogram_t1_mri)
        self.ax_hist.set_yticks([])
        self.ax_hist.set_autoscaley_on(True)
        self.ax_hist.set_prop_cycle('color', cfg.color_histogram_t1_mri)
        self.ax_hist.set_title(cfg.title_histogram_t1_mri, fontsize='small')

or 'both' (using both aseg and aparc stats).

    Default: {}.
    \n""".format(cfg.t1_mri_features_OLD))

    help_text_disable_outlier_detection = textwrap.dedent("""
    This flag disables outlier detection and alerts altogether.
    \n""")

    in_out = parser.add_argument_group('Inputs', ' various ways to provide input')

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

    in_out.add_argument("-m", "--mri_name", action="store", dest="mri_name",
                        default=cfg.default_mri_name_T1w_generic, required=False,
                        help=help_text_mri_name)

    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("-b", "--bids_dir", action="store", dest="bids_dir",
                        default=None,
                        required=False, help=help_text_bids_dir)

    out_spec = parser.add_argument_group('Outputs',
                                         'options related to outputs')

def add_alpha_slider(self):
        """Controls the transparency level of overlay"""

        # alpha slider
        ax_slider = plt.axes(cfg.position_slider_seg_alpha,
                             facecolor=cfg.color_slider_axis)
        self.slider = Slider(ax_slider, label='transparency',
                             valmin=0.0, valmax=1.0, valinit=0.7, valfmt='%1.2f')
        self.slider.label.set_position((0.99, 1.5))
        self.slider.on_changed(self.set_alpha_value)

sub001
        sub002
        cn_003
        cn_004

    \n""")

    help_text_image_names = textwrap.dedent("""
    Specifies the names of 3d images to be QCed.
    \n""")

    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_delay_in_animation = textwrap.dedent("""
    Specifies the delay in animation of the display of two images (like in a GIF).

    Default: {} (units in seconds).
    \n""".format(cfg.delay_in_animation))

    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(cfg.default_views[0], cfg.default_views[1], cfg.default_views[2]))

    help_text_num_slices = textwrap.dedent("""
    Specifies the number of slices to display per each view. 
    This must be even to facilitate better division.

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)

    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)

    vis_args.add_argument("-a", "--alpha_set", action="store", dest="alpha_set",
                          metavar='alpha', nargs=2,
                          default=cfg.default_alpha_set,
                          required=False, help=help_text_alphas)

    outliers = parser.add_argument_group('Outlier detection',
                                         'options related to automatically detecting possible outliers')
    outliers.add_argument("-olm", "--outlier_method", action="store",
                          dest="outlier_method",
                          default=cfg.default_outlier_detection_method, required=False,
                          help=help_text_outlier_detection_method)

    outliers.add_argument("-olf", "--outlier_fraction", action="store",
                          dest="outlier_fraction",
                          default=cfg.default_outlier_fraction, required=False,
                          help=help_text_outlier_fraction)

    outliers.add_argument("-olt", "--outlier_feat_types", action="store",
                          dest="outlier_feat_types",