Human mesh created from MRI scan. Issues with arm rigging.


I am working on a research project for a University. We have a human body mesh created from an MRI scan. I am currently trying to rig the skin, so that I can put the limbs in different positions. The legs work pretty good, but I am having issues with the arms; mainly in the under-arm area. This is my first time using Blender, so I was wondering if someone could please take a look at the skin mesh file. I think the guy’s arms were too close to his body during the MRI scan. The skin mesh basically has no armpit, so it stretches the torso (like wings) when I lift the upper arm. Is this fixable, or just a bad mesh to try and rig? I tried weight painting, but it didn’t help. I removed double vertices in edit mode and that helped with mesh tearing, but made the distortion issue worse. Does anyone have any suggestions? Maybe a different software? In desperation, I cut out the armpit area of the mesh (where the arm meets the torso) as a test. The arm looked better when raised, but now I have a huge whole in the mesh. Therefore, that’s not a practical solution.

Thank you!


Normally when you make a human form you would make it in “T” pose with the arms horizontal out to the side, then rig it with a Rigify armature (this is an add-on) and then parent the armature to the mesh “With Automatic Weights”. After that you can tweak the weights in Weight Paint mode.

I cannot tell exactly what is wrong from your images and would need the blend file - you can upload just the required bits (mesh and armature) to then post the link here for us to look at. You have not told us how meany vertices there are or whether these are Tris (three sided faces) or Quads (for sided and the recommended format for Blender).

But from what I can see, the armature is not correct in that it looks like the shoulder and upper arms are not pivoting in the correct location to get a proper deform. I could do with seeing an image of the armature to check this. Also it appears that you have no shoulder bones - these will stop the upper shoulder muscles dropping when you raise the arm.

The mesh tearing is caused by gaps in the topology that need mending - this is going to be very difficult as the model is not in T pose. You can achieve this T pose by posing the armature to T pose, then applying it so it permanently deforms the mesh to T pose. After that you can repair the mesh and then re-parent the mesh to the armature and work from there. You will need to very the weights of the upper arm bones to the thorax since these are also deforming the thorax along with the thorax bone(s), before you apply the armature.

Really I need to see the armature and mesh to be able to tell you in more detail what you can do to correct the problems. In particular I need to see the armature and the topology of the mesh, a rendered view does not show me where the vertices are…

Oh yes “Welcome to BA” - please note that while images give us some indication of the problems, they do not let us see the problem itself, this can only be accomplished by posting the blend file.

Can I recommend that you also search out Nathan Vegdahl’s “Humane Rigging” tutorials - these will give you an excellent insight into how to rig and animate biped forms.

Cheers, Clock.


Thank you for your support! I uploaded the file to However, I’m not sure how to generate a URL for sharing? After the file was done uploading, I copied the URL from my browser. Here it is:

I believe this link will allow you to download the file. This model contains an armature, various human bones, and the outer layer of the human skin. The file size was originally 60 MB, so I had to delete a lot of parts to get it down to < 30 MB for uploading. The meshes are all unedited (i.e., all original geometry that was downloaded). Most parts have been parented to the armature, all using automatic weighting.

I located the armature bone pivot points using the actual human skeleton. My idea was to locate the pivot points in the correct spots (or as close as possible by eye). As you mentioned, the shoulder gets a lump when you raise the arm. The only way I have been able to fix this, is to lower the shoulder pivot point in the armature. I hate to do that though because that’s not where the shoulder actually pivots!

I am a machine design engineer by trade, so I am used to 3D CAD, like SolidWorks. I am finding it difficult to work with blender because things drastically deform we I rotate the limbs. I am used to working with rigid bodies constrained in CAD assemblies. For example, the ball end of the humerous (upper arm bone) shrinks and grows when I rotate the arm. That looks bogus. Ideally, I’d like the bones to hold their shapes and only have the skin deform.

Now that you have the files, is the mesh geometry bad (unusable?) and/or is my armature faulty (any advice?)?

Thank you for your help!

, Mech Jess

OK I will download this and look at it the next few days, I am up to my neck in work just now. One thing, if you file is 60Mb for one human, I suspect you have way too many vertices. Can I suggest you get a copy of MakeHuman, run it and make yourself a human character, then go to User Prefs in Blender => Add-ons tab and enable MakeHuman Add-on. Then import the MakeHuman project into blender and see what the mesh looks like. If you also specify the Rigify skeleton on the MakeHuman project you will see what a really good armature looks like as well. MakeHuman in freeware, just do an Internet search for it.

I know where you are coming from with the CAD thing, I came from a long Cad background and had to adapt a little, but that background enables me to make some pretty good mechanical models in Blender.

Until later,

Cheers, Clock.

I took a quick look. In my opinion this mesh is not suitable for rigging. It resembles a sculpted mesh with far too many vertices, and very poor edge flow.

A typical workflow to use a mesh like this is to use it as a mannequin for retopology. A new and simpler mesh with quad topology and proper edge flow would be created by snapping new faces, vertices and edge loops onto the sculpt. The new mesh would then be rigged. With a variety of methods materials could be added to fake the details of the sculpted mesh without adding to the complexity of the new simplified base mesh.

Rigging the simplified mesh will give you many advantages like, easier weight painting, improved performance in the 3d view for animation or posing, decreased file size, easier corrective shapes for deformations, etc.

I’m sure that was not the answer you were looking for. Just throwing it out there. As I said, it’s just my opinion.

Good luck!

OK This may be helpful to you:

This is what a good mesh should look like, I cannot get your file yet - Internet overused here by spotty kids watching crap youtube videos in the village I guess. :mad: I have saved the file for you so you can play with it - look at the armature as well, this is quite complex, but VERY capable and can work in either IK or FK mode. You could look at the help for the Rigify armature. You need to add the “Import .mhx” add-on in User Prefs to load MakeHuman models if you make your own.

Here is the blend file URL:

Note! it is only 5Mb, yet renders really nice. You can even add a sub surf modifier if you want smoother or more detailed form. I have done nothing more than import the MakeHuman model into Blender. I have not included all the image texture files - you will find these in the same directory that you export your MakeHuman model to. I guess you don’t need to worry about these just yet…

Cheers, Clock. :slight_smile:

EDIT: I forgot to say that I agree with what @Danpro has said - a file that big must have far too many vertices to ever be able to animate.