help > Displaying thresholded connectome results
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Jan 25, 2018  01:01 PM | alexandre boutet
Displaying thresholded connectome results
Dear Surf Ice experts,

Reading the mediawiki, I understand that it is not ideal and difficult to display thresholded results on a surface. However, I am trying to show differences between 2 connectomes, connectome A and connectome B. I find it intuitive to for example, threshold >0 and binarise connectome A and B and subsequently do "A minus B" and looked at the results.

Results of non thresholded and smooth connectome A are displayed in the attached file (top left). Results of non thresholded and non smooth connectome A are displayed in the attached file (top right).

Now if I display the thresholded connectome A with smoothing (bottom left), it looks markedly different than either top left or top right (as explained din the mediawiki). If I display the thresholded connectome A without smoothing (bottom right), it looks similar but "pixelated".

My question is: Is there a solution when using thresholded results to avoid this "exaggeration of the results" with the smoothing but at the same time having a "nice" display of the results (avoid the pixelation). Or is there no good real compromise...
Attachment: figures.png
Mar 3, 2018  08:03 AM | Chris Rorden
RE: Displaying thresholded connectome results
This seems to be an issue with how you are thresholding your images. The input images have the intensity range -0.1289..0.2294 (left) and -0.1453..0.2361 (right). The masks you created appear to be forced to be binary (0 or 1). The discontinuous values will be particularly influenced based on your smoothing setting for interpolation. This issue is described in depth here:
  https://www.nitrc.org/plugins/mwiki/inde...

I think you have a couple solutions. First, you want to preserve the values in your NIfTI images. It is hard to give a precise solution without seeing your images, but this solution looks useful:
  https://github.com/rordenlab/spmScripts/...
the other alternative is to save each mesh as mz3 and then use Matlab to mask the vertex colors. That may be a nicer solution, but it is more complicated.