That's not easily possible because you'd need to heavily modify the slideshow generator class in wp-content\themes\choices\includes\helper-slideshow.php. Another solution would be to replace the slideshow call in header.php with your shortcode - so i.e. replace:
if(!empty($avia_config['slide_output']))
{
echo "<!-- ####### SLIDESHOW CONTAINER ####### -->";
echo "<div id='slideshow_big' class='slideshow_color container_wrap ".avia_is_dark_bg('slideshow_color', true)."'><span class='top_stripe_shadow'></span>";
echo "<div class='container'>".$avia_config['slide_output']."</div></div>";
}
with.
$sliderdata = do_shortcode('[myslider]');
if(!empty($avia_config['slide_output']))
{
echo "<!-- ####### SLIDESHOW CONTAINER ####### -->";
echo "<div id='slideshow_big' class='slideshow_color container_wrap ".avia_is_dark_bg('slideshow_color', true)."'><span class='top_stripe_shadow'></span>";
echo "<div class='container'>".$avia_config['slide_output']."</div></div>";
}
else if(!empty($sliderdata ))
{
echo "<!-- ####### SLIDESHOW CONTAINER ####### -->";
echo "<div id='slideshow_big' class='slideshow_color container_wrap ".avia_is_dark_bg('slideshow_color', true)."'><span class='top_stripe_shadow'></span>";
echo "<div class='container'>".$sliderdata."</div></div>";
}
and instead of [myslider] insert your shortcode.