How to show the body field in a custom template?
Your code should be:

    &lt;?php
// We hide the comments and links now so that we can render them later.
hide($content['comments']);
hide($content['links']);
//$original_image = file_create_url($node-&gt;field_portfolio_images['und'][0]['uri']);
$lightboxrel = 'portfolio_' . $nid;
$portfolio_images = field_get_items('node', $node, 'field_image');
$first_image = '';
if ($portfolio_images) {
  foreach ($portfolio_images as $k =&gt; $portfolio_image) {
    if ($k == 0) {
      $first_image = file_create_url($portfolio_image['uri']);
    } else {
      $image_path = file_create_url($portfolio_image['uri']);
      print '&lt;a href="' . $image_path . '" rel="prettyPhoto[' . $lightboxrel . ']" style="display:none"&gt;&amp;nbsp;&lt;/a&gt;';
    }
  }
}
?&gt;
&lt;div id="node-&lt;?php print $node-&gt;nid; ?&gt;" class="portfolio-text &lt;?php print $classes; ?&gt; clearfix"&lt;?php print $attributes; ?&gt;&gt;
&lt;?php print render($title_prefix); ?&gt;
&lt;?php print render($title_suffix); ?&gt;
&lt;div class="ImageWrapper content"&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;div class="portfolio-images"&gt;
        &lt;?php print render($content['field_image']); ?&gt;
    &lt;/div&gt;
    &lt;div class="ImageOverlayLi"&gt;&lt;/div&gt;
    &lt;div class="portfolio-overlay"&gt;            
        &lt;div class="portfolio-inner"&gt;
            &lt;div class="portfolio-info"&gt;
                &lt;div class="portfolio-tools"&gt;
                   &lt;a href="&lt;?php print $first_image;?&gt;" rel="prettyPhoto[&lt;?php print $lightboxrel;?&gt;]" data-toggle="tooltip" data-original-title="&lt;?php print t('View Image');?&gt;" data-placement="bottom" class="zoom dtooltip"&gt;&lt;span class="fa fa-expand"&gt;&lt;/span&gt;&lt;/a&gt;
                &lt;/div&gt;              
            &lt;/div&gt;
        &lt;/div&gt;
    &lt;/div&gt;
&lt;/div&gt;
&lt;div class="portfolio-description"&gt;
    &lt;h3 class="name"&gt;&lt;?php print $title; ?&gt;&lt;/h3&gt;
    &lt;?php print render($content['body']); ?&gt;
&lt;/div&gt;        
&lt;?php //print render($content['links']); ?&gt;
&lt;?php //print render($content['comments']); ?&gt;