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| * TBD | * Ahmet will continue with his action items this week. * Katie spent time working on parametric representation segmentation. The related specifications were updated. * Snehal, with Craig's help, wrote a script to read and plot tissue testing files. A test file should also be uploaded to test the script if/when it is updated. * Snehal is working on the video down-sampling script now. Craig notes the script should be generic enough for the user to specify key parameters such as sampling frequency, duration, number of frames, etc. * The eye wash station was built. Once the area is cleaned up, the equipment can be moved. Snehal will need help moving the equipment. |
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| * TBD | * The BioMomentum software was updated. Snehal ran tension LCL test for 20 minutes and it appears the erroneous data point issue is not present. This seems to be resolved but it will be checked in upcoming tests. * Related to tissue testing, Ahmet notes the protocols need to be worked out in detail in the upcoming two and a half weeks (before WCB 2014). One bottle neck for completing this task is working out the tissue grips, especially for ligament tension testing. Snehal notes there has been slippage at the clamp interface in the past and this issue needs to be troubleshot, which includes potentially manufacturing a new clamp. Most of the samples for testing have been acquired, the testing protocols need to be worked out and Snehal will reach out to the group members for help with these items. Testing will start today, with an update next week. * Snehal created a new page to document the approach to tissue thickness measurement. Ahmet will help Snehal update this section and the other tissue testing specifications. Ahmet will also review the tissue specimen preparation specifications. |
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| * TBD | * Craig created a relational modeling graph. This was uploaded to the wiki (ModelingModelGraph page). The relationships were discussed and it was agreed the graph is nearly complete. Katie will create a version of this graph that is specific to her project, which highlights the relational components that she needs for her ACL/PCL study. * Katie will also see how her project fits into the Modeling and Simulation Workflow. We discussed the relationship between her project and the overall specification needs of Open Knees. Katie gave an update of her project directly from the specific wiki site. Katie learned to identify the cruciates and orient herself with regards to common anatomical descriptions (anterior, medial, superior). Katie, with Craig's help and training, also gave an update on her experience using Slicer 3D. She noted the program seems to randomly create backup files of the segmented volumes. This should be troubleshot. Both volumes and surface (stl) can be saved from Slicer. Smoothing can also be performed on the segmented volumes (documented in this wiki). Regarding smoothing of the stl files, meshlab was explored. Katie found that the geometry can be smoothed though we need to come up with a way to quantitatively compare the end product (if it's a nurbs surface) with the original segmentation. Ahmet noted that Salome can calculate the distance between any point and a surface. This may be a possibility to measure the final parametric surface with the unsmoothed stl. The path to create parametric surfaces is also being explored. Rhino appears to work well for this (Katie downloaded a trial) and Ahmet would like pyformex to also be explored. Minus a parametric surface, Ahmet believes Truegrid can be used with an stl file. Stl files can be a fallback, if it is found to work in Truegrid. Regarding parametric surfaces, an unstructured parametric (patches) or a structured parametric (lofted) representation can be defined. Ultimately, this path will be resolved to efficiently create hexahedral meshes of the desired structure(s). |
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| * TBD | * Action items were discussed and agreed on; see Immediate Action Items above. |
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| * TBD | * None noted. |
Recurring Meeting of Cleveland Clinic Core Team
Date: June 18, 2014
Time: 10:30 AM EST
Means: In person meeting
Attendees:
- Ahmet Erdemir
- Jason Halloran
- Craig Bennetts
- Snehal Chokhandre
- Katie Stemmer
Agenda:
- Discuss immediate action items from the last meeting.
- Discuss tissue testing progress.
- Discuss modeling specifications progress.
- Decide immediate action items for the next meeting.
- Other.
Immediate Action Items:
- Ahmet
- Talk to Biomomentum Inc. about downsampling approach for the video data.
- Update imaging parameters and release anatomical imaging specifications.
- Update experimentation workflow figure.
- Review tissue testing specifications.
- Review tissue sampling section of specimen preparation specifications.
- Craig
- Review specimen preparation specifications.
- Robb
- Find camera positioning system for thickness measurements.
- Provide processing tools to move between "right knee abstraction" and physical representation" of knee data collected during joint testing.
- Tara
- Review tissue testing specifications.
- Jason
- Revisit pressure calibration specifications.
- Snehal
- Provide a test file to accommodate scripts for reading tissue testing system data.
- Write a Python script to downsample number of video images collected during tissue testing.
- Start planning and executing tissue testing procedures to finalize tissue testing specifications.
Notes:
- Discuss immediate action items from the last meeting.
- Ahmet will continue with his action items this week.
- Katie spent time working on parametric representation segmentation. The related specifications were updated.
- Snehal, with Craig's help, wrote a script to read and plot tissue testing files. A test file should also be uploaded to test the script if/when it is updated.
- Snehal is working on the video down-sampling script now. Craig notes the script should be generic enough for the user to specify key parameters such as sampling frequency, duration, number of frames, etc.
- The eye wash station was built. Once the area is cleaned up, the equipment can be moved. Snehal will need help moving the equipment.
- Discuss tissue testing progress.
The BioMomentum software was updated. Snehal ran tension LCL test for 20 minutes and it appears the erroneous data point issue is not present. This seems to be resolved but it will be checked in upcoming tests.
- Related to tissue testing, Ahmet notes the protocols need to be worked out in detail in the upcoming two and a half weeks (before WCB 2014). One bottle neck for completing this task is working out the tissue grips, especially for ligament tension testing. Snehal notes there has been slippage at the clamp interface in the past and this issue needs to be troubleshot, which includes potentially manufacturing a new clamp. Most of the samples for testing have been acquired, the testing protocols need to be worked out and Snehal will reach out to the group members for help with these items. Testing will start today, with an update next week.
- Snehal created a new page to document the approach to tissue thickness measurement. Ahmet will help Snehal update this section and the other tissue testing specifications. Ahmet will also review the tissue specimen preparation specifications.
- Discuss modeling specifications progress.
Craig created a relational modeling graph. This was uploaded to the wiki (ModelingModelGraph page). The relationships were discussed and it was agreed the graph is nearly complete. Katie will create a version of this graph that is specific to her project, which highlights the relational components that she needs for her ACL/PCL study.
- Katie will also see how her project fits into the Modeling and Simulation Workflow. We discussed the relationship between her project and the overall specification needs of Open Knees. Katie gave an update of her project directly from the specific wiki site. Katie learned to identify the cruciates and orient herself with regards to common anatomical descriptions (anterior, medial, superior). Katie, with Craig's help and training, also gave an update on her experience using Slicer 3D. She noted the program seems to randomly create backup files of the segmented volumes. This should be troubleshot. Both volumes and surface (stl) can be saved from Slicer. Smoothing can also be performed on the segmented volumes (documented in this wiki). Regarding smoothing of the stl files, meshlab was explored. Katie found that the geometry can be smoothed though we need to come up with a way to quantitatively compare the end product (if it's a nurbs surface) with the original segmentation. Ahmet noted that Salome can calculate the distance between any point and a surface. This may be a possibility to measure the final parametric surface with the unsmoothed stl. The path to create parametric surfaces is also being explored. Rhino appears to work well for this (Katie downloaded a trial) and Ahmet would like pyformex to also be explored. Minus a parametric surface, Ahmet believes Truegrid can be used with an stl file. Stl files can be a fallback, if it is found to work in Truegrid. Regarding parametric surfaces, an unstructured parametric (patches) or a structured parametric (lofted) representation can be defined. Ultimately, this path will be resolved to efficiently create hexahedral meshes of the desired structure(s).
- Decide immediate action items for the next meeting.
- Action items were discussed and agreed on; see Immediate Action Items above.
- Other.
- None noted.