Differences between revisions 7 and 8
Revision 7 as of 2018-05-25 13:49:27
Size: 2112
Editor: ricimorrill1
Comment:
Revision 8 as of 2019-02-19 18:20:02
Size: 2970
Editor: ricimorrill1
Comment:
Deletions are marked like this. Additions are marked like this.
Line 9: Line 9:
 1. Download the desired registration markers and bone STLs (place in folder named mri-oks00x, where x is the specimen ID).
   * 3 registration marker stls for tibia
   * 3 registration marker stls for femur
   * stl for tibia bone
   * stl for femur bone
 1. Create registration xml ([[https://simtk.org/svn/openknee/utl/Registration/Registration_final/oks001_registration_01.xml| Example Registration XML]])
 1. Download the desired registration markers and bone STLs (place in folder named geometry-oks00x, where x is the specimen ID).
   * For tibiofemoral joint mechanics:
     *
3 registration marker stls for tibia
     * 3 registration marker stls for femur
     * stl for tibia bone (only needed for visualization)
     * stl for femur bone (only needed for visualization)
   * For patellofemoral joint mechanics (in addition to TF joint mechanics):
     * 3 registration marker stls for patella
     * stl for patella (only needed for visualization)
 1. Add digitizing order of femur and tibia in a [[https://simtk.org/svn/openknee/utl/Registration/Registration_final/ReadMe_Notes.txt|ReadMe_Notes.txt]] file within the main Configuration folder of the tibiofemoral test directory.

 1. Create registration xml ([[https://simtk.org/svn/openknee/utl/Registration/Registration_final/oks001_registration_01.xml| Example Registration XML]]). Place in registration-00x_xx folder within the registration-00x directory.
Line 18: Line 23:
     * Inputs:
        * Registration xml
        * Boolean: 0-does not show visualization figure, 1-shows visualization figure
     * Outputs:
        * Transformation matrices saved within .npz file for each trial that has processed data.

Target

  1. Create visualization of experimental tests in modeling (image) coordinate system.
  2. Prepare experimental data for model inputs.

Registration

  1. Download joint mechanics .zip file from Downloads page.
  2. Download the desired registration markers and bone STLs (place in folder named geometry-oks00x, where x is the specimen ID).
    • For tibiofemoral joint mechanics:
      • 3 registration marker stls for tibia
      • 3 registration marker stls for femur
      • stl for tibia bone (only needed for visualization)
      • stl for femur bone (only needed for visualization)
    • For patellofemoral joint mechanics (in addition to TF joint mechanics):
      • 3 registration marker stls for patella
      • stl for patella (only needed for visualization)
  3. Add digitizing order of femur and tibia in a ReadMe_Notes.txt file within the main Configuration folder of the tibiofemoral test directory.

  4. Create registration xml (Example Registration XML). Place in registration-00x_xx folder within the registration-00x directory.

  5. Run script from command line Registration Script

    1. Change directory to desired OpenKnee specimen (e.g. oks001)

    2. Run convert_to_image_CS.py <oks00x_registration_0x.xml> <1>

      • Inputs:
        • Registration xml
        • Boolean: 0-does not show visualization figure, 1-shows visualization figure
      • Outputs:
        • Transformation matrices saved within .npz file for each trial that has processed data.

Example using oks001 - 004_passive flexion
White stls - segmentation from MRI. Colored registration marker stls - spheres from calculated center of digitized points.
OK_reg1.png

Re-sample Data for Model Input

  1. Create text file with desired tdms file(s) you would like to re-sample. Place this text file in either the KinematicsKinetics directory of the PatellofemoralJoint or TibiofemoralJoint mechanics directories depending on which data you are interested in re-sampling. Example text file for PatellofemoralJoint

  2. Place in the appropriate directory KinematicsKinetics of either the TibioFemoral or PatelloFemoral test directories.

  3. Run script from command line Re-sampling Script

    1. Change directory to desired OpenKnee specimen (e.g. oks001)

    2. Run resampling_plotting.py <oks00x_registration_0x.xml> <oks0x_xF.txt>

See Sample Passive Flexion Video for video example.

Specifications/ModelingKinematicsKinetics/Discussion (last edited 2019-02-19 18:20:02 by ricimorrill1)