3D rendering options?



Hello all,

Is there a way to select different 3D rendering options of overlays in mrview? I like the automatic “volume rendering” achieved by loading an overlay, but I would like better definition, like the one obtained with surfaces or vtk renderings (E.g. right vs. left in image below).

In other discussions thread I saw some screenshots from @rsmith from the connectome toolbox where the rendering of the ROI is exactly what I am looking for.

Is there a way to achieve that without running the connectomics analysis? I could create a vtk mesh for the label/mask i want to 3D render, but I couldn’t figure out how to open it in mrtrix. It looks like mrview has the rendering capability to do this, but I haven’t found a way :woman_facepalming:

Thank you in advance for your help,




I don’t know if this would be useful for you.

I usually smooth my overlays using fsl command (-kernel gauss). That way, I have a nice smoothed overlay in the 3D render mode of mrtrix. I just have to adjust the thresholds and the transparency of the structure. I work with the basal ganglia and for me this works perfect. Hope this helps!



No, currently the ability to render meshes is limited to the connectomics tool, unfortunately. The issue has been raised before, but as always, the problem is developer time and priorities.

That said, @josue_avecillas’ suggestion is a good one, I often use a similar strategy. Only difference is you can achieve it without FSL using the mrfilter command, e.g.:

mrfilter overlay.nii smooth overlay_smooth.nii