Personalize model based on CT data

#1

Hello,
I would like to personalize my model based on CT data.

STAGE 1 - I think I did it correctly.

I made scaling transformations of RBF and STL according to lesson 3 (https://anyscript.org/tutorials/Scaling/lesson3.html)
(folder CT_kosci for bone source “AnyBody.stl” and target “KNUTH_mm.stl”) and I received (in my opinion) a good result in the form of file "KNUTH_AnyBody.stl.

STAGE 2
Then, in accordance with Lesson 4 (https://anyscript.org/tutorials/Scaling/lesson4.html) I tried to scale the model according to the guidelines. And unfortunately I have problems with this step.
I did it in 2 ways

    1. THE FIRST MODIFICATION: I tried to replace the AnyBody.stl bone with KNUTH_AnyBody.stl (which I received from STAGE 1), automatically selecting vertices
    1. THE SECOND MODIFICATION: I followed the instructions from lesson 4 (https://anyscript.org/tutorials/Scaling/lesson4.html)

However, I did not get a good bone scaling and I not received bone the same as from CT data called “KNUTH_mm.stl”. The bone after scaling is smaller and a little thinner compared to standard scaling. The cervico-shaft angle is not preserved, the stem more resembles the source bone. This will not allow me to properly modification the muscle attachments and will be influence the result of muscle forces and joint reaction force.

3)Using the “StandingModelScalingDisplay” option, the situation is the same.

I checked various RBF functions, but the model with RBF _Triharmonic function looks best and “reasonably”
I tried to do it myself for several weeks, but to no availch :sob:. However, I gave up because I do not know what I’m doing wrong. That’s why I am asking for help, how should I personalize my model based on image data.
I attach the link with my model (https://transferxl.com/08j1bc9JsSm5vd). I am using the new version of AMMR, TLEM 2.0

Thank you very much for your help.:grinning:
Best regards,
Justyna

1 Like
#2

Hi Justyna,

I looked at your code. Probably the problem is that the tutorial was written using TLEM1.1 femur bone. Hence it does not work with TLEM2.1 right away. I loaded all your source surfaces and they did not match the AnyBody TLEM2.1 femur. This will lead to strange looking morphing.

  1. Source femur should be a non-scaled AnyBody femur of the dataset of your choice.
  2. It should be exported in local ref. frame - do not use “AnyBody_Standing”.
  3. Landmarks used in standalone morphing should be reused in the model inclusion (in your case there are a lot of differences between your separated morphing and the inclusion part).

Otherwise the code looks good.

Kind regards,
Pavel

P.S. We should update the tutorial. Thank you for reminding and sorry for not explicitly specifying this fact.

1 Like
#3

Hello,

Currently, I’m personalized my model in plug-in-gait-simple model based on the CT. I was wondering is it a good move that I first scaled the model based on the height and mass and then I used the morphing tech in tutorials for the detailed thigh and shank segment?
You said the source femur should be the non-scaled femur, I want to know more about the process of scaling.

Any help would be appreciated!
Thank you!

Best Wishes,
Lee

Comparison the EMG to simulation
#4

Hello Lee,

You should define the subjects’ height and weight, and additionally include the code outlined in Tutorial 15: Personalize Your Model (Lesson 2). Yes the source femur STL should be the non-scaled femur (the TLEM 2.0 cadaver bone geometry in the local coordinate system). Then your target femur needs to have the same topology as this bone, this thread may be helpful (https://forum.anyscript.org/t/patient-specific-model-with-mocap-model/2688/10).

Best Regards,
Christine

#5

Hello,

I’m planning to use Plug_in_gait_simple LowerExtremity model to scale the right femur and tibia, the code you mentioned about height and mass are in the Lowerextremity.any, and I include the code in tutorials 15, is it a right move in the picture?

I don’t know if the STL in Plug-in-gait model is non-scaled or not.
Thank you!

Best Wishes,
Lee

#6

Hi Lee,

Bones in mocap models will always be scaled to some extend to match the subject in the recording.

Best regards
Søren

#7

Hello,

I want to scale the femur and tibia bone of right leg in Plug-in_gait_Simple model to simulate the TKA, and I don’t get the workflow of scale.
Should I change the body mass and height first and then custom scale the femur and tibia (How should I get the source bone since it scaled automatically based on the recording data). I’m a little confused about the workflow of scaling bones in the plug-in-gait-simple model, would you mind sharing the idea?

Thank you!
Any help would be appreciated!

Best regards,
Lee

#8

Hi Lee,

In order to get the ‘source_STLs’ for the femur and tibia you need to load the StandingModel.main.any example (AMMR\Application\Examples\StandingModel). Then make sure in the BodyModelConfiguration.any file there is no scaling, you will probably have to change

#define BM_SCALING SCALING_XYZ_ --> #define BM_SCALING SCALING_NONE_

Once that is all set you can double click on the femur and go into the model tree and then right click on the AnyDrawSurf folder in the model tree and click ‘Export Surface’, make sure to do so in the local coordinate system. Then do the same for the tibia.

Could you describe the workflow you are trying to accomplish and which software tools you are using in order to obtain your target_stls (subject-specific stls)? With this information I can then best advise you how to continue in the Plug-in_gait_Simple model with the morphing process.

Kind Regards,
Christine

Comparison the EMG to simulation
#9

Hello,

Thank you for your response.
I’m trying to build my own gait model with TKA based on the essay:

Marra, Marco A., et al. “A Subject-Specific Musculoskeletal Modeling Framework to Predict In Vivo Mechanics of Total Knee Arthroplasty.” Journal of Biomechanical Engineering 137.2(2015):020904.

And I’m using the same software mentioned in the essay except for the newer version of Anybody and 6th Grand Challenge Competition Data.

I still want to know more about the rigid-body registration after morphing.

Thank you!
Best Regards,
Lee

#10

Hi,

I couldn’t find the code you mentioned above in StandingModel, and there is no BodyModelConfiguaration.any.

Do you mean StandingModelScalingDisplay or standingModel?

Thank you!
Best Regards,
Lee

#11

Hi Lee,

I will try answer your question,

I think Christine was referring to the StandingModel.

I just checked this model in most recent AMMR and it do have a file called “BodyModelConfiguration.any”

Best regards
Søren

#12

Hello,

Thank you for your response.

I found the “BodyModelConfiguration.any” in the new AMMR 2.2.1, I was wondering if the non-scaled bones are the same in AMMR2.1.1 and AMMR 2.2.1 for I am using the AMMR2.1.1?

Best Regards,
Lee

#13

Hi Lee,

There should be no changes in the shape of the unscaled bones between these versions, but i can not rule out that there could be differences in the re-solution.

Best regards
Søren

#14

Hello,

I used the bones you and Christine mentioned above.
I did it well based on lesson 1 from personalizing your model in tutorials 15.
image

When I used it in the plug-in-gait model follow the code in lesson 2 from tutorials 15, it didn’t work well.
image

I believe I have used the wrong bone. What is the specific bone as generic bone?

Thank you!

Best Regards,
Lee

#15

Hi Lee,
The tutorial was written using the TLEM1 femur. You need to use the TLEM2 one to make it work. We recently changed the default to be TLEM2.

Please right click and export TLEM2 femur surface on an unscaled model.

Kind regards,
Pavel

#16

Hello,

The differences are only the bones( TLEM1 &TLEM2 ) or the code differs too?
Recently I’m trying to use the standingModelSclingDisplay None-scale bones to scale, is it right move?

Thank you!

Best Regards,
Lee

#17

The landmarks should be selected accordingly. But the code stays the same.
Yes, StandingModelScalingDisplay with ScalingNone should be perfect.
P.

#18

Hello,

I believe I did well in lesson1 from tutorials 15.
image

However, It didn’t look right when I use it based on the lesson 2.

I changed the Transform to STLTransform, it showed the same as above.
I changed it to RBFTransform, it showed a little reasonable.

A little confused!

Best Regards,
Lee

#19

Hi Lee,

Can you share what you have in the ‘MyScalingFunctionFemur.any’ file please?

Best Regards,
Christine

#20

/* This file defines a subject-specific morphing law for the Lesson 4 of Scaling tutorial*/

AnyFolder MyScalingFunctionFemur = {

AnyFunTransform3DLin Transform = {
ScaleMat = {{1,0,0},{0,1,0},{0,0,1}};
Offset = {0,0,0};
PreTransforms = {&.STLTransform, &.ReverseTransform};
};

AnyFunTransform3DLin2 AffineTransform =
{
//PreTransforms = {};
Points0 = …TSeg2ScaleFrame(
{
{0.0776166,-0.38519,0.0434183},
{0.0291691,-0.388362,0.0489085},
{0.0702968,-0.375534,-0.0240044},
{0.0171157,-0.195817,0.013274},
{-0.0481888,-0.00649841,0.00942058},
{0.009532983,0.016264,-0.015843}
});
Points1 =
{
{-0.0335496,0.00561388,-0.0159026},
{0.0131622,0.0129517,-0.0401973},
{0.00955101,0.0160026,0.0352691},
{0.0253999,0.200918,-0.0145758},
{0.0797432,0.417332,-0.022623},
{0.0356885,0.431939,0.0166936}
};
Mode = VTK_LANDMARK_AFFINE;
};

AnyFunTransform3DLin2 ReverseTransform = {
Points0 = .AffineTransform.Points1;
Points1 = .AffineTransform.Points0;
Mode = VTK_LANDMARK_RIGIDBODY;
};

AnyFunTransform3DRBF RBFTransform =
{
PreTransforms = {&.AffineTransform};
RBFDef =
{
Type = RBF_ThinPlate;
Param = 1;
};
Points0 = …TSeg2ScaleFrame(
{
{0.0776166,-0.38519,0.0434183},
{0.0874067,-0.392876,0.0191814},
{0.0291691,-0.388362,0.0489085},
{0.0336871,-0.401527,0.0528365},
{0.0702968,-0.375534,-0.0240044},
{0.0840476,-0.405399,-0.0240044},
{0.046656,-0.36353,0.00203508},
{0.0519064,-0.422182,0.045868},
{0.6825022,-0.426252,-0.0176293},
{0.0171157,-0.195817,0.013274},
{-0.0153646,-0.0538598,-0.00275116},
{-0.0111436,-0.0677822,-0.000322446},
{-0.0481888,-0.00649841,0.00942058},
{0.009532983,0.016264,-0.015843},
{-0.0060929,-0.0615546,0.00151425},
{-0.036961,-0.0406715,0.053172},
{-0.038943,-0.0406992,0.0101967},
{0.0005855,-0.0509986,0.0225059},
{0.0885529,-0.388669,0.00365604},
{0.0606754,-0.420174,-0.0318583},
{0.055317,-0.422778,-0.00984486},
{0.0349846,-0.423029,0.0426269},
{0.052857,-0.420594,0.0475201},
{0.080049,-0.370333,0.0108282},
{0.0708826,-0.371049,0.0418323},
{0.0353599,-0.347786,0.0276989},
{0.0536242,-0.343088,0.00172468},
{0.0827935,-0.39489,-0.0240079},
{0.0169421,-0.390191,0.0277442},
{0.0162501,-0.410556,0.0348857},
{0.0284323,-0.386989,0.0139395},
{0.0177057,-0.398845,0.0187154},
{0.0389646,-0.396279,-0.025363},
{0.0888908,-0.401907,-0.00876824},
{0.0548423,-0.397694,0.054172},
{0.077992,-0.421114,0.00714761},
{0.0463893,-0.284064,0.011615},
{0.0632637,-0.3013,0.0116601},
{0.0558027,-0.254465,0.0189366},
{0.0487975,-0.316967,0.00655951},
{0.0640665,-0.335391,0.00255428},
{0.0535251,-0.272982,0.0154517},
{0.0405198,-0.22445,0.0146546},
{0.0213611,-0.169527,0.0158975},
{0.0377727,-0.194215,0.0374407},
{0.0502173,-0.234592,0.0301236},
{0.0506393,-0.239614,0.0207116},
{0.0231513,-0.417397,0.0260686},
{0.0774498,-0.38116,0.0283361},
{0.0749767,-0.375019,0.0308108}
});
Points1 = {
{-0.0335496,0.00561388,-0.0159026},
{-0.0280022,-0.00269058,0.0120236},
{0.0131622,0.0129517,-0.0401973},
{0.012141,-0.000433684,-0.0446263},
{0.00955101,0.0160026,0.0352691},
{0.00075525,-0.0115942,0.0405223},
{0.0119686,0.0280065,0.0120921},
{-0.00935188,-0.0231205,-0.0279828},
{-0.00432023,-0.02776477,0.0308913},
{0.0253999,0.200918,-0.0145758},
{0.0585843,0.361284,0.000857341},
{0.0550661,0.346257,-0.00206488},
{0.0797432,0.417332,-0.022623},
{0.0356885,0.431939,0.0166936},
{0.0503574,0.351978,0.00110147},
{0.06372,0.381583,-0.0571084},
{0.0809548,0.383419,-0.0216873},
{0.0338266,0.35835,-0.0121963},
{-0.024259,0.00394552,0.0217401},
{0.0194315,-0.0242202,0.0356052},
{0.0178418,-0.0246098,0.0145176},
{0.00503235,-0.0230989,-0.0367033},
{-0.0103818,-0.0219988,-0.0288968},
{-0.0198254,0.0267586,0.01261},
{-0.0264373,0.024819,-0.0170189},
{0.0114769,0.0436825,-0.0237335},
{0.00778656,0.0454752,0.00969556},
{0.00118152,0.00134793,0.0426428},
{0.0293845,0.00573355,-0.0302668},
{0.0303841,-0.00849202,-0.0380678},
{0.024226,0.00585466,-0.00989906},
{0.0320057,-0.0066778,-0.0235614},
{0.0327069,-0.00420313,0.0239168},
{-0.0118756,-0.0072693,0.0340803},
{-0.013875,0.00182269,-0.0345471},
{-0.0159371,-0.0209117,0.0101429},
{0.00910361,0.107057,-0.000237901},
{-0.0108107,0.083166,0.00767706},
{-0.00792776,0.133574,-0.00168584},
{0.00402107,0.0750955,0.00614671},
{-0.00431338,0.0517168,0.0142384},
{-0.00429717,0.115213,0.0035777},
{0.00607966,0.182325,-0.00565917},
{0.0207678,0.241608,-0.0108694},
{-0.00150775,0.198673,-0.0232213},
{-0.00827493,0.154543,-0.0107971},
{-0.0024134,0.158461,-0.00343703},
{0.0208062,-0.0232439,-0.0270419},
{-0.0251027,0.00861673,-0.00121048},
{-0.0240169,0.0216748,-0.00427663}
};
BoundingBox =
{
Type = BB_Cartesian;
ScaleXYZ = {2, 2, 2};
DivisionFactorXYZ = 5*{1, 1, 1};
};
BoundingBoxOnOff = On;
};

AnyFunTransform3DSTL STLTransform =
{
PreTransforms = {&.RBFTransform};
RBFDef.Type = RBF_ThinPlate;
AnyFixedRefFrame Input = {
AnySurfSTL SourceSurf = {
FileName = “femur211.stl”;
ScaleXYZ = {1, 1, 1};
};
AnySurfSTL TargetSurf = {
FileName = “TargetFemur.stl”;
ScaleXYZ = {1, 1, 1};
AnyFunTransform3D &pre = …TSeg2ScaleFrame;
};
};

SurfaceObjects0 = {&Input.SourceSurf};
SurfaceObjects1 = {&Input.TargetSurf};
NumPoints = 400;
BoundingBox.ScaleXYZ = {2, 2, 2};
BoundingBox.DivisionFactorXYZ = {1, 1, 1};
BoundingBoxOnOff = On;

};

}; // MyScalingFunctionFemur