open-discussion > Deeper activations
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Mar 8, 2016 04:03 PM | gaelj
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.
Gaƫl.
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.
Gaƫl.
Nov 1, 2016 03:11 PM | 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
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