Effects of stress-dependent growth on evolution of sulcal direction and curvature in models of cortical folding
Description
Input files of ABAQUS (can be read into the ABAQUS or can be used to create the same simulation in similar programs such as FEBio) with necessary codes and links to reproduce the output.
Files
Steps to reproduce
After running the simulation and getting the final output file, you can run the python script “ExtractPointsFromABAQUS”. Just update the ODB file name and directory in the code. This script will create three text files containing the mid-cortical surface points, x,y, and z coordinates. In the next step, you must run the python script “TextToExcel” to put all the data in an excel file before importing it to MATLAB. Make sure that directory in the code matches the correct working directory. Then read the excel into Matlab with IETM After this, run the script Main2 to get the points to form a complete and find the connectivity between points. The output will provide data to create a triangulated surface for all the frames. Then you can use the code in the following link to get the curvatures on each surface (need a slight modification to get the principals( and if you want higher accuracy, using two ring neighborhood can help. https://www.mathworks.com/matlabcentral/fileexchange/61136-gaussian-and-mean-curvatures-calculation-on-a-triangulated-3d-surface Then you can run cluster or cluster2 script to get the points that belong to a sulci region and use Paraview to select the starting point and ending point of each sulcus. Then import the points into Matlab again and run the fast marching method to get the baseline of the sulcus. Here is the link to the fast marching method https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching