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    <p>You can adjust the transparency so lower values are more transparent. First, you need the handles to your slices:</p> <p><code>h = slice(X,Y,Z,V,sx,sy,sz);</code></p> <p><code>h</code> is not a single handle but a series of handles to the different slices. For any one handle you can change the transparency (or loop around for all n to change them all):</p> <p><code>set(h(n),'alphadata',get(h(n),'cdata'),'facealpha','flat')</code>;</p> <p><code>alphadata</code> is the data for transparency - by default this is "1" (opaque), so instead for each handle you can set it to the contents of <code>cdata</code>. <code>AlphaDataMapping</code> should already be set to <code>scaled</code> by default - so the values in <code>alphadata</code> are mapped to an alphamap, just as <code>cdata</code> values are mapped to your colormap (more on that later).</p> <p><code>facealpha</code> is a setting for how the alphadata is applied to the faces of an object - needs to be changed so that the values in alphadata are actually used.</p> <p>If you want to adjust how transparent values are or which are transparent, you can change the alphamap. The default map is just linear and can be seen by <code>plot(get(gcf,'Alphamap'))</code>, where is 0 = invisible and 1 = opaque. The length of the map can vary so you have a lot of freedom in adjusting it - for example you can completely zero out the lower part if you're not interested in those values:</p> <pre><code>a = alphamap('rampup',256); a(1:80)=0; alphamap(a); % only changes alphamap of current figure </code></pre> <p>Read more about transparency in Matlab <a href="http://www.mathworks.co.uk/help/matlab/visualize/making-objects-transparent.html" rel="nofollow">here</a>.</p>
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