NeuroSurgSim/TCon-Meetings

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Regular Meetings 2014-01-09 On the agenda: 1. Team members quick status 2. Make sure everyone know how to push branches (topics) and commits to their repositories Summary of our TCon (1/9/2014): Status Reports: 1. Ricardo has a very simplified prototype for the simulator. 2. Fotis is working on a sofa plugin that will allow for the meshing of the brain and pathologies 3. Sreekanth is working on the interfaces for the corotational fem 4. Andinet is working on the preprocessing pipeline and has preliminary results that involve skull-stripping with 3DSlicer. Also, UNC IRB declared we do not need any special approval to receive retrospectively acquired AVM patient data so we will be getting this data very soon. Ricardo will set up a private repository for the AVM data in our Midas server. Ricardo will be following up with the technical team and have a session on how to create git branches and topics and push their branches to the repository. 2013-12-23 On the agenda: 1. How is the technical team doing in terms of familiarization with sofa. 2. Discuss backlog list for our first coding sprint (starting on Jan 1). The main task is to agree on the items we want to work on and focus for the sprint. Prototype (Kitware) Create FEM interface classes (RPI) Implement addForce and getPotential (RPI) Handle both linear and nonlinear constitutive models (RPI) Create interface for pre-processing pipeline (segmentation-meshing) (Kitware, ODU) Generate mesh for sample label map of the brain (ODU) Mesh smoothing (ODU) Collision detection interfaces (UNC) Implement bounding tree generation routine (UNC) Incorporate self collision into the data structure (UNC) Summary of our TCon (12/23/2013): Status Reports: 1. Ricardo is working on the pre-processing pipeline: Writing script to fetch necessary libraries to do segmentations: ITK, VTK, TubeTK. 2. Andinet working on getting IRB going at UNC so we can get data form UNC hospitals. Will be working on setting up Sofa and compiling it on Windows and Linux. 3. Fotis & Nikos are working on the meshing capabilities, they created meshes for a sample brain scan with tumor, will be working on integrating their software with Sofa. 4. Dinesh is in contact with the Sofa folks, we might get a Sofa developer to work on the collision pipeline by mid January or February. 5. Sreekanth worked on the sofa examples and is getting familiar with the FEM interfaces. 6. Today Ganesh Sankaranarayanan (from RPI) joined the conversation, he will be supervising from the RPI side and working with Sreekanth. These are the tasks we decided to work on for our first coding sprint: 1. Create FEM interface classes (RPI) 2. Implement addForce and getPotential (RPI) 3. Couple with the corotational FEM to model arteries and vessel-like structures (#1 and #2 RPI) 4. Create interface for pre-processing pipeline (segmentation-meshing) (KITWARE ) 5. A dummy SOFA Neurosurgery simulation app (KITWARE) 6. Have the meshing software ready for integration ( MESHING: ODU ) 7. Collision detection interfaces ( Use what is currently available in SOFA ) Ricardo is going to follow up with the technical team via chat sessions at the beginning of January to coordinate and discuss more. 2013-12-12 On the agenda: 1. Building SOFA: Windows and Unix 2. Software process: Explain how contributions are going to make it to the main development branch (commit messages, pull requests, software review process and merge contributions) 3. Deliverables: Discuss how modules are going to be incorporated and integrated. Summary of our TCon (12/12/2013): Status Report: 1. Ricardo is working on the preprocessing pipeline: brain and vasculature segmentation and mesh generation with BrainVISA, TubeTK. 2. Sreekanth is working on familiarizing with sofa's codebase and FEM and is working on preparing an example app. 3. Fotis is also working on a sample application on which he loads a generated mesh into sofa. Fotis is going to use a mesher developed at ODU and will generate meshes for segmented brain data. 4. Dinesh is in contact with the SOFA developers and getting them involved on writing a continuous collision detection algorithms that integrates with SOFA collision pipeline. He mention the possibility of having a SOFA developer coming to the GAMMA lab to work on this implementation. 5. We discussed the timeline a bit more, you can see the document here: ​[Specific Goals and Deadlines](https://docs.google.com/a/kitware.com/spreadsheet/ccc?key=0ApC_y6Y3RlVndHhLX0VqTjVSbEdOSW5mTURQeXZ0cGc&usp=drive_web) This document has details of the deliverable and timeline we set at the kickoff-meeting.