Hello all- I am a new slicer.

doing a project to assess displacement of bone with time to create a joint kinematic model model.

How can I measure the displacement of bones with time using transformation.

Slicer stores linear transforms as 4x4 homogeneous transformation matrix.

You can retrieve translation of the coordinate system origin (4th column of the matrix) or rotation of each coordinate system axis (rotated coordinate system axes are stored as the first 3 columns of the matrix).

For these to make sense anatomically, make sure to choose the origin of the coordinate system with a meaningful position (e.g., approximate center of rotation of the joint) and axes with anatomical axes (e.g., principal axes of a bone). To achieve this, you can compute a transform from user-defined landmarks points (1. center of the joint, 2. a point on the first principal axis, 3. a point on the second principal axis) and apply that transform to all bones.

Thanks. But how would I make sure the use defined landmark points are the same from one frame to the other. @lassoan- Professor Andras Lasso- would it be easy if I share my data set to set up the scene. Thanks

One option is to choose your landmarks as anatomical points that you can accurately identify on each image.

Another option is to specify landmarks in one image. Then you can use image intensity or surface based registration to transform all images to the reference image.