Computational Modeling & Simulation of Atria with Fibrotic Remodeling - Example

Computational Modeling &amp; Simulation of Atria with Fibrotic RemodelingExample prepared by Dr. Patrick M. Boyle ([e-mail]) 2021-02-24<br>Update 2021-05-03: removed junk OSX files from zip; updated to reflect testing info (openCARP on OSX works!), and added version number (v2.2) to meshalyzer documentation.<br>Available in perpetuity via fig share doi: 10.6084/m9.figshare.14347979<br>###############################################################################Step 1: Download the publicly available mesh###############################################################################<br>This should be obtained from the following repository:https://zenodo.org/record/3764917#.YDc13XVKjS8If this work is re-used, please attribute the original source properly:Roney et al. Med Image Anal. 2019 Jul;55:65-75. PMID: 31026761.<br>Only one of the meshes will be used (LA_Epi/A/Labelled_A_6_1)... but the whole .zip archive should be downloaded and decompressed in thesame directory as this file.<br>###############################################################################Step 2: Run the included shell script to modify the mesh###############################################################################<br>$ bash -u CreateMesh_AvgFibroticLA.sh<br>If any required files are missing, the script should output an informative error<br>###############################################################################Step 3: Run the simulations using a compiled version of openCARP###############################################################################<br>The model has been tested using openCARP v5.0 compiled on various linux systemswith default settings. It was also recently tested with a compiled version onMac OSX. Only built-in components of the simulator are used. openCARP is freeto use for non-commercial applications, but use of the simulator is governed bythe terms of use outlined at https://opencarp.org/<br>Recommended syntax to run:$ [mpi prefix] [carp path] +F [name].par |tee [name].log 2&gt;&amp;1<br>Example wrapper code for running all 15 simulations:$ for F in AvgFibroticLA_Stim*par; do mpiexec -n 32 /opt/openCARPv5.0/bin/openCARP.opt +F $F \ |tee $(basename $F .par).log 2&gt;&amp;1;done;<br>Each simulation will take several minutes to run (e.g., max. 15 minutes when runon a supercomputer node with 32 cores). Based on testing at the time of examplepreparation, the RIPV1 pacing site should induce reentry sustained by a rotor inthe vicinity of the RSPV region (with meander in the LA roof).<br>###############################################################################Step 4: Visualize results using meshalyzer (state files supplied)###############################################################################<br>Compile and install meshalyzer (also available via openCARP site).This version of the example has been tested with meshalyzer v2.2; if you use anolder version, the visualization should still work but you may see warnings atlaunch time regarding items in the .mshz file (these can be ignored).<br>Example command for visualizing mesh only:$ meshalyzer AvgFibroticLA. fib.mshz<br>Example command for visualizing simulation results:$ meshalyzer AvgFibroticLA. AvgFibroticLA_LSPV1/vm.igb vm.mshz

伴纤维化重构的心房计算建模与仿真示例
本示例由Patrick M. Boyle博士（[e-mail]）于2021年2月24日编制
2021年5月3日更新：移除压缩包内无用的macOS系统文件，更新内容包含测试信息（macOS平台可正常运行openCARP），并为meshalyzer文档添加版本号v2.2
本数据集可通过Figshare永久获取，DOI：10.6084/m9.figshare.14347979
###############################################################################步骤1：下载公开可用的网格模型###############################################################################
该网格模型可从以下仓库获取：https://zenodo.org/record/3764917#.YDc13XVKjS8
若复用本工作，请正确标注原始来源：Roney等人，《医学图像分析》（Med Image Anal.），2019年7月；55卷：65-75。PMID：31026761
本示例仅使用其中一个网格模型（LA_Epi/A/Labelled_A_6_1），但需下载完整的.zip压缩包，并将其解压至与本文件相同的目录下
###############################################################################步骤2：运行内置Shell脚本以修改网格模型###############################################################################
执行命令：$ bash -u CreateMesh_AvgFibroticLA.sh
若存在缺失的依赖文件，脚本将输出带有提示信息的错误内容
###############################################################################步骤3：使用编译版openCARP运行仿真实验###############################################################################
本模型已在多种Linux系统上使用编译版openCARP v5.0（默认配置）完成测试，近期也在macOS平台的编译版openCARP上完成了测试。仿真仅使用模拟器的内置组件。openCARP可免费用于非商业用途，但模拟器的使用需遵循https://opencarp.org/中公布的使用条款
推荐的运行命令格式：$ [MPI前缀] [openCARP路径] +F [参数文件名].par |tee [日志文件名].log 2>&1
批量运行全部15组仿真的示例脚本：$ for F in AvgFibroticLA_Stim*par; do mpiexec -n 32 /opt/openCARPv5.0/bin/openCARP.opt +F $F |tee $(basename $F .par).log 2>&1;done;
每组仿真需运行数分钟（例如，在配备32核的超级计算机节点上运行时，最长耗时约15分钟）。根据本示例编制时的测试结果，RIPV1起搏位点可诱发由RSPV区域附近的转子维持的折返激动（左心房顶部可见折返路径漂移）
###############################################################################步骤4：使用meshalyzer可视化仿真结果（附带状态文件）###############################################################################
请编译并安装meshalyzer（该工具也可从openCARP官网获取）
本示例已在meshalyzer v2.2版本上完成测试；若使用旧版本，可视化功能仍可正常运行，但启动时可能会出现关于.mshz文件内容的警告信息，此类警告可忽略
仅可视化网格模型的示例命令：$ meshalyzer AvgFibroticLA_fib.mshz
可视化仿真结果的示例命令：$ meshalyzer AvgFibroticLA AvgFibroticLA_LSPV1/vm.igb vm.mshz