@Tak Hi, I did some progress on weekend but didn't finish the video. It takes longer to do than I thought, but that's no problem, I still want to finish it and didn't forgot about it.

I changed the proportions of the mesh - like length of legs, arms, locations of joints etc. The armature is defined by the points and I found the mesh not to correspond with that armature - the joint placement was not where the joints of armature were. I changed the mesh proportions in edit-mode with proportional editing.

"You also mentioned that this can be done using a trained neural network, and yes I have several similar .c3d files with same naming consistency, so how this can be done?" - If there is naming consistency the solution is the same as with creating the bones - you have there a hierarchy tree of the armature that the script takes as input to produce all the bones. There can be similar hierarchy describing constraints for the script to take as input.

Both these methods won't work in general case however when the structure or naming is different. Then there is the possibility to train a neural network on some examples - then it should be able to recognize patterns of markers (like arms, spine, head,..) and rig them correctly independent from naming.

There is TensorFlow which is opensource library for machine learning and has python API - with this it is doable but a lot of work.

@Jerryno Hi, Thank you so much for that.

So I can't just bake the animation to the armature and then move it and put it in Tpose?

I've actually tried that but the results were horrible, but may be I did something wrong?

"I was thinking to bake the armature's animation before applying Tpose as it will be easier to adjust it's Tpose through the bones not the points, would that be okay?" - to be able to pose the bones by themselves you would have to delete all the constraints. So you would need to delete constraints, pose the armature into Tpose, apply it as Rest pose then recreate the constrains again to move the bones by the c3d points.

moving the points is less convenient but you don't have to delete and recreate the constraints.

Changing the Rest pose effects the animation because it changes the bones starting reference state. So if you bake the animation into bones, then change the Rest position, it will ruin the baked animation

mmm, so this means even if I baked then recreated the constraints it won't work, right?

the constraints would override the baked animation completely, it will work, but then there is no need to bake it because of it. I think only the .bvh export needs baked keyframes (not 100% sure) to export the animation, so the baking should be the last step before export. No need to bake animation before changing the Rest pose.

oh okay, so I can bake put the armature in Tpose using the bones (as I find it very hard to do it with the points) then re-constraint right? because after setting the Tpose as rest position and the mesh is parented to the armature and be animated smoothly, I want be able to control the armature from it's bones, so it won't be a problem baking the animation and modifying the bones rotation using the bones, right?

@Tak Yes, correct. You can bake, that will remove constraints, then you can change the Tpose with bones, then apply it rest-pose, that will ruin the baked animation, so you then re-constrain and bake again.

and I'll apply the same constraints which was before baking right?

@Jerryno I also don't understand how I can select the correct bone alignment axis, like for example, why My_T4SpinalProcess was aligned to -X while other bones to X?

@Tak That depends where the point that is used for aligning is located and which axis is the best to lock onto it. The points are all over the place and I chose the axes so that all the bones in a bone chain would be oriented about the same. This will be in the video so you can see how and why I chose those specific axes.

@Jerryno That's great. Thank you so so much.

And if you could please include IK for may be like one arm, one leg and spine, and how I can limit the rotation of each bone with a certain limit so that for example if I grabbed the righthandIK bone toward the shoulder I don't want the upperarm angle to be unrealistic I want to know how I can set the max and min value of the rotation of each bone, so if you can just demonstrate it to me just for one bone to understand and know how it can be done.

I'm really very thankful and grateful for helping and teaching me. One day I'll come to Czech Republic and will give you a gift in person :)

You know what? two years ago I was in Europe visiting part of the family living there. And I visited Germany, Poland, Slovakia and Austria and was planning to visit Czech next but I didn't have the time and had to go back for studies, but my brother visited it and he liked it.

So I'll make sure next time it will be included in my route and I'll let you know beforehand here :)