Smoothing a complex object without affecting borders

Hi all,

I’ve been working on MRI scans of a mouse cortex (I know this might sound weird, but this is for work!).
The cortex of a mouse is smooth (unlike the human one) and it is therefore important to keep it smooth.
The cortex has been segmented in several sub-regions using Slicer3D and the sub-volumes have been exported as Obj files in Blender. So far, so good, except that the file was HUGE (800 MB).

I simplified the meshs by using the decimate modifier, then used the smooth Vertex tool to get a smaller file (~50 MB). I did just a bit of additional smoothing in scult mode to get something real smooth!

I am mostly happy with the result I obtained, except that some “cracks” have appeared between my cortical regions. so, the cortex does not look smooth anymore, but it sort of look deconvolute and start resembling a human brain (well, sort of!). This is because the edges of my cortical regions are not sharp anymore.

I’ve tried many things to smooth the surface of the cortical regions, without affecting their edges, but nothing so far has worked.

Any ideas on how to proceed?

I have attached 2 pictures. the first one shows the original cortex (top view) with the cortical subregions (red lines), the the result of the decimate + smooth vertex steps, see the cracks appearing. The second file the result of the smooth in scult mode… with these cracks between regions increasing in size.

Thanks in advance for your help!



Hi looks interesting…

I guess the question is what is the final usage for the model?

Im guessing that the model is going to need some retopology… id suggest searching for shrinkwrap retopolgy maybe…

or share a part of your blend file and someone will quickly be able to give you better advice.

Drop me a pm if you are not comfortable sharing it.

Hi Hesskay, thanks for the quick reply.

the model is for teaching purposes, to highlight brain regions and explain what signal their process (visual, motor…), their hierarchy (primary vs. secondary vs. associative brain regions)… Those anatomy courses are boring, and I hope that this will make them a bit more interesting/intuitive!

I can send you a blend file. I made one in which I removed most of the cortical regions. only 7 are left, but the file is still very large (85 MB), too big to attach it to this post. I can send you it via a server.

Yes retopology might be the way to go, but this may be very time consuming. I have not much experience with that. Decimate and smoothing only took me an hour for all brain regions. I guess that retopology would take longer. Maybe with the shrinkwrap approach…

have a good day

use edge creases the double subdivide

Hi fdfxd,
thanks for the tip.
I’ll try with edge creases. Might be difficult to select the edge as the model is super complex and full of small cubes, but I’ll have a go.
Not sure I understand the second part of you sentence: “then double subdivide”; you probably meant " then apply double smooth vertex". just to be sure, so that I don’t miss any tip.


a faster way would to just go to “select> sharp edges” then play arround with the “angle” a bit then hit shift + e then hit 1,

Double subdivide is just adding one Subdivision modifier then duplicating it.
as you can imagine it’s going to tank your performance if you’re not careful

can you upload model in first post if not too big !

you could retopo it
it would give better topo with quads
and easier to work with
or use Remesh modifier

but this soft is probably better for remeshing
Meshlab for great remesh

if you have slices you could use these and make a 3D model too in blender
but without using mesh data using voxels!

also this script here

happy bl