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This page provides specifications of knee specimen '''OKS001'''. This is a (possibly osteoarthritic) elderly male specimen candidate.
<<TableOfContents>>
== Specimen Characteristics ==
Right knee
'''Gender:''' ''Male''
'''Age:''' ''71 years''
'''Race:''' ''White ''
'''Height:''' ''1.83 m''
'''Weight:''' ''77.1 kg''
'''BMI:''' ''23.1''
'''Serologically tested:''' ''Yes''
'''X-Ray:'''
. {{attachment:oks001_1.png}}
== Experimentation ==
-- [[aerdemir]] <<DateTime(2014-10-06T13:35:28Z)>> All, please complete relevant sections of this page during and after experimentation.
=== Specimen ===
'''Reference Specification:''' [[Specifications/Specimens]] - [[http://wiki.simtk.org/openknee/Specifications/Specimens?action=recall&rev=40|Revision as of October 5, 2014]]
'''Leading Team Member:''' Snehal Chokhandre
'''Supporting Team Members:''' Ahmet Erdemir
'''Timeline:''' October 5, 2014
'''Data Location:''' In this page.
'''Protocol Deviations:'''
1. None.
'''Notes:'''
1. None.
=== Specimen Preparation ===
'''Reference Specification:''' [[Specifications/SpecimenPreparation]] - [[http://wiki.simtk.org/openknee/Specifications/SpecimenPreparation?action=recall&rev=124|Revision as of October 6, 2014]]
'''Leading Team Member:''' Tara Bonner
'''Supporting Team Members:''' Snehal Chokhandre, Craig Bennetts, Robb Colbrunn, Eryn Merico
'''Timeline:''' Thawing: 12:30 PM October 5, 2014 - 10:00 AM October 6, 2014; Dissection: 11:30 AM - ~ 1:30 PM October 6, 2014 (specimen need to thaw for another hour); Assembly of Optotrak base plugs ; Assembly of Registration Markers; Probing of Anatomical Landmarks; Probing of Registration Markers.
'''Data Location:''' On this page
'''Protocol Deviations:'''
1. Quadriceps tendon was prepared (specifically its suturing) during the initial preparation.
1. 1. Registration Markers - Digitization. Digitization order for femur spherical markers are: --(1 - anteromedial, 2 - medial, 3 - lateral)-- 1 - lateral, 2 - medial, 3 - posterior (-- [[aerdemir]] <<DateTime(2017-04-21T12:39:16Z)>> During data analysis, the order of digitization for femur registration markers were corrected). Digitization order for tibia spherical markers are: 1 - lateral, 2 - medial, 3 - posterior. Note that the order of digitization for tibia markers is a deviation from the specifications. Nonetheless, this order is the same for oks004. THIS IS A CANDIDATE FOR UPDATING THE SPECIFICATIONS FOR ALL REMAINING SPECIMENS.
1. Femur and tibia was cut 7.5 inches from the epicondylar line (rather than 8 for femur, 7 for tibia) THIS IS A CANDIDATE FOR UPDATING THE SPECIFICATIONS FOR ALL REMAINING SPECIMENS.
'''Notes:'''
1. Plastic screws for registration markers are #8-32 (drill bit diameter 0.136 (for tapping), tap size #8-32, drill wire gage 29), need to include this in the specifications.
1. Brass screws for base plugs are #3 (use drill bit diameter ~.088 in, no tapping), need to include this in the specifications.
1. Patella Optotrak base plug orientation was not specified in specifications; two screw holes should be on the inferior side, need to include this in the specifications.
1. The order of probing divots on the patella registration marker assembly was not documented in specifications, need to include this in the specifications.
=== Joint Imaging ===
==== Specimen Preparation ====
'''Reference Specification:''' [[Specifications/SpecimenPreparation]] - [[http://wiki.simtk.org/openknee/Specifications/SpecimenPreparation?action=recall&rev=124|Revision as of October 6, 2014]]
'''Leading Team Member:''' Craig Bennetts
'''Supporting Team Members:''' Snehal Chokhandre
'''Timeline:''' 8.30 am, October 7,2014 - 9.30 am, October 7,2014
'''Data Location:'''
'''Protocol Deviations:'''
1. The posterior region of the knee was dissected further (removal of skin, fat, and muscle layers) to allow fitting of the whole specimen and the patellafemoral registration marker assembly in the transportation fixture (therefore the knee coil of the MRI).
'''Notes:'''
1. The tibia end of foam to secure the tibia during transportation and imaging had to be cut lower to accommodate fitting of the whole specimen and the patellofemoral registration marker assembly in the transportation fixture (therefore the knee coil of the MRI).
==== Imaging ====
'''Reference Specification:''' [[Specifications/ExperimentationAnatomicalImaging]] - [[http://wiki.simtk.org/openknee/Specifications/ExperimentationAnatomicalImaging?action=recall&rev=118|Revision as of October 6, 2014]]
'''Leading Team Member:''' Craig Bennetts
'''Supporting Team Members:''' Snehal Chokhandre, Sam Doerle, Ahmet Erdemir
'''Timeline:''' 10.00 am-12.00 am, October 7, 2014
'''Data Location:'''
Data was received from the imaging facilities and uploaded to in-house data management server (http://cobicore.lerner.ccf.org/midas; only accessible within Cleveland Clinic network). Raw DICOM files were stored in the folder Open Knee(s) --> Private --> oks001 --> MRI --> DICOM
DICOM files were converted to NIfTI files, stored in the folder Open Knee(s) --> Private --> oks001 --> MRI --> NIFTI of the in-house data management server. NIfTI files were also disseminated to the public in the 'Downloads' section of the project website, https://simtk.org/home/openknee, under the package oks001.
Data storage and dissemination were accomplished based on the updated imaging specifications, see [[http://wiki.simtk.org/openknee/Specifications/ExperimentationAnatomicalImaging?action=recall&rev=118|Revision as of April 16, 2015]].
'''Protocol Deviations:'''
1. None
'''Notes:'''
* General purpose imaging
{{attachment:general-purpose.png}}
* Cartilage imaging
{{attachment:cartilage.png}}
* Connective tissue imaging
{{attachment:connective-tissue.png}}
=== Joint Mechanics ===
==== Equipment Preparation ====
'''Reference Specification:''' [[Specifications/PressureCalibration]] - [[http://wiki.simtk.org/openknee/Specifications/PressureCalibration?action=recall&rev=16|Revision as of October 6, 2014]]
'''Leading Team Member:''' Robb Colbrunn
'''Supporting Team Members:''' Ahmet Erdemir
'''Timeline:''' October 6, 2014 (Equilibration: 10:20 AM - 11:20 AM; Calibration: 11:30 AM - 12:30 PM)
'''Data Location:'''
'''Protocol Deviations:'''
1. None.
'''Notes:'''
1. C-Line lamination sheet was used to seal the sensor. Put one sheet with sticky side up, roll the sensor over it. Put another sheet with sticky side up, roll the sensor+sheet over it. Trim edges.
1. For equilibration: 5051-P1-11111DT1-1200
1. For equilibration: 6.35 Bars (maximum possible).
1. Need to change data storage information in equilibration to reflect the workflow.
1. Equilibration file (2-pass) name 5051-P1-11111DT1-1200_10-6-14_6 bar.equ. (available in oks001/configuration folder of the pressure sensor data collection computer.
1. During calibration, the use of 2-pass equilibration file was problematic. Second pass was deleted from the file and a new equilibration file was created 5051-P1-11111DT1-1200_10-6-14_6 bar-single_pass.equ, which was used in calibration.
1. Pre-testing calibration file name 5051-P1-11111DT1-1200_10-6-14_6 bar.equ. (available in oks001/configuration folder of the pressure sensor data collection computer.
==== Specimen Preparation ====
'''Reference Specification:'''
'''Leading Team Member:''' Tara Bonner
'''Supporting Team Members:''' Robb Colbrunn
'''Timeline:''' Oct. 7 12:30-2:30
'''Data Location:'''
'''Protocol Deviations:'''
1. None.
'''Notes:'''
1. None.
==== Testing ====
'''Reference Specification:''' [[Specifications/ExperimentationJointMechanics]] - - [[http://wiki.simtk.org/openknee/Specifications/ExperimentationJointMechanics?action=recall&rev=91|Revision as of October7, 2014]]
'''Leading Team Member:''' Tara Bonner
'''Supporting Team Members:''' Robb Colbrunn
'''Timeline:''' Tibiofemoral (Oct. 7, 2:30-5:30), Patellofemoral (Oct. 8, 11:00-12:45)
'''Data Location:'''
Data was received from the robotics testing facility and uploaded to in-house data management server (http://cobicore.lerner.ccf.org/midas; only accessible within Cleveland Clinic network). Zipped folders were stored in the folder Open Knee(s) --> Private --> oks001 --> !JointMechanics under relevant joint related folders.
Zipped folders were extracted and organized in the dissemination folder under Open Knee(s) --> Private --> oks001 --> !JointMechanics --> DISSEMINATION of the in-house data management server. DISSEMINATION folder was downloaded and disseminated to the public in the 'Downloads' section of the project website, https://simtk.org/home/openknee, under the package oks001.
Data storage and dissemination were accomplished based on the updated joint mechanics testing specifications, see [[http://wiki.simtk.org/openknee/Specifications/ExperimentationJointMechanics?action=recall&rev=101|Revision as of August 25, 2015]].
'''Protocol Deviations:'''
1. None.
'''Notes:'''
1. Used a 10 second hold for Varus/Valgus torque and Ant/Post drawer (in laxity testing)
1. Used a 14 second hold for Int/Ext rotation torque (in laxity testing)
1. Version of simVITRO software used was unreleased revision 3024 of the repository. The files can be found in svn://dev.lerner.ccf.org/data1/svn/repos/colbrunn-svn/Projects/Numbered Projects/2013CB-031 Open Knee/Original simVITRO-Tested on oks001 oks002 oks003 oks004
=== Tissue Mechanics ===
==== Specimen Preparation ====
'''Reference Specification:''' [[https://simtk.org/plugins/moinmoin/openknee/Specifications/SpecimenPreparation?action=recall&rev=164| Revision as of Jan 5,2017]]
'''Leading Team Member:''' Snehal Chokhandre
'''Supporting Team Members:'''- None
'''Timeline:''' Jan 5,2017 -
'''Data Location:''' MIDAS(oks001/TissueMechanics)
'''Protocol Deviations:'''
1. None
'''Notes:'''
1. Started with lateral femoral condyle cartilage.
1. Any non-uniformity of sample thickness is going to adversely affect the test data.
==== Testing ====
'''Reference Specification:''' [[https://simtk.org/plugins/moinmoin/openknee/Specifications/ExperimentationTissueMechanics?action=recall&rev=170| Revision as of Jan 05, 2017 ]]
'''Leading Team Member:''' Snehal Chokhandre
'''Supporting Team Members:'''- None
'''Timeline:''' Jan 5, 2017 -
'''Data Location:''' MIDAS(oks001/TissueMechanics)
'''Protocol Deviations:'''
1. For Lateral femoral condyle cartilage compression tests (both unconfined and confined), 10-15% strain was used for preconditioning. Mainly to keep the sample from floating away in unconfined compression.
'''Notes:'''
1. For details and updates see, [[https://simtk.org/plugins/moinmoin/openknee/Roadmap|Roadmap]] Tissue Testing dashboard and [[https://simtk.org/plugins/moinmoin/openknee/RecurringMeetings/2017-01-10-Update|Cleveland Clinic core team recurring meetings 2017-01-10-Update]]
== Data Analysis ==
=== Registration ===
==== Spherical Markers ====
1. Femur
1. <Posterior>oks001_MRG_FMR-P_RAW_02.stl
1. <Lateral>oks001_MRG_FMR-L_RAW_02.stl
1. <Medial>oks001_MRG_FMR-M_RAW_02.stl
1. Tibia
1. <Posterior>oks001_MRG_TBR-P_RAW_02.stl
1. <Lateral>oks001_MRG_TBR-L_RAW_02.stl
1. <Medial>oks001_MRG_TBR-M_RAW_02.stl
1. Patella
1. <Superior>oks001_MRG_PTR-S_RAW_01.stl
1. <Lateral>oks001_MRG_PTR-L_RAW_01.stl
1. <Medial>oks001_MRG_PTR-M_RAW_01.stl
==== Digitizing Order ====
1. Tibia:
* Sphere 1 = Lateral
* Sphere 2 = Medial
* Sphere 3 = Posterior
1. Femur:
* Sphere 1 = Lateral
* Sphere 2 = Medial
* Sphere 3 = Posterior
=== Joint Mechanical Testing ===
Pictured below are the Anterior Posterior laxity graph, IR/ER laxity graph, and the Varus/Valgus laxity graph.
{{attachment:oks001_1LaxitGraphs.png}}
== Modeling & Simulation ==
=== Segmentation ===
=== Geometry Generation ===