open-discussion > Deeper activations
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Mar 8, 2016  08:03 AM | Gaël Jobard
Deeper activations
Hi,

I've been unsuccessfully looking for the 'search depth' setting of mricron in mricroGL. I love the quality of the render in mricroGL, but have not yet found a satisfactory way of displaying activations that are slightly under the brain surface.
I join an illustration of what I can do with mricron and the best I can achieve with mricroGL. Note that the parietal activations are not easy to see on the mricroGL rendering, do you have a way of improving this that I did not see ?
Thank you for your help.

Gaël.
Attachment: render.png
Nov 1, 2016  08:11 AM | Chris Rorden
RE: Deeper activations
With the latest version of MRIcroGL (30Sept2016) you control overlay depth with the "overDistance" and "overAlpha" sliders (assuming you are using the "Default" shader). You may also want to switch the shader from "Default" to one of the "overlay_*" shaders (e.g. overlay_shell or overlay_glass).

For visualizing deep activations, a surface renderer (e.g. Surf Ice) displaying a mesh may be nicer than a volume renderer (MRIcroGL):
  https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Overlay_a_normalized_SPM_or_FSL_statistical_map_that_has_been_converted_to_an_iso-surface_mesh
  https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Scripting_a_mesh_overlay