Wondering if I can create segmentation label from imported STL object?

[Shangcheng_Wang]

Hi community,

I had a MRI data set and segmented bone models in STL format. Could I create segmentation label from these 3D models?

I also imported a cylindrical pin (create from CAD software) into slicer, and I am wondering I could map the pin into segmentation label. So I can see if the pin would damage tendon or muscle on its path.

Any idea or comment?

Thanks

[lassoan (Andras Lasso)]

You can convert a model to segmentation mode by right-clicking on it in Data module then choosing conversion to segmentation.

You can also import models to existing segmentation node using Segmentations module.

[Shangcheng_Wang]

Hi Andras,

I am able to convert model to segment node, but I can not see it in slice and 3D, see picture below.

Thanks
Sam

[lassoan (Andras Lasso)]

Probably the STL file is defined in LPS coordinate system. Slicer assumes it is in RAS. Try transforming the model from LPS to RAS coordinate system by applying a transform as described here:

DICOM and VTK file orientation Issue

Most common issue is LPS/RAS coordinate system mismatch. So, may try to convert your data from LPS to RAS coordinate system by transforming it using Transforms module by a matrix that has [-1,-1,1,1] in the diagonal: [image]

[Shangcheng_Wang]

Hi, you are right. That solves my problem. Thanks very much.

Sam