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Installation and set-up

System Requirements

  • Simnibs
  • Python 3.6
  • nibabel
  • numpy
  • Matlab
  • Workbench Command

Instructions

  1. Clone Simnibs Cifti Tools from https://github.com/DCAN-Labs/simnibs_cifti_tools

System Requirements for MSI user

  • Singularity
  • Simnibs
  • Python 3.6
  • nibabel
  • numpy
  • Matlab
  • Workbench Command

Set up for MSI user

  1. There is a current working version that was cloned from the github repo (https://github.com/DCAN-Labs/simnibs_cifti_tools) located at /panfs/roc/groups/8/faird/shared/code/internal/pipelines/simnibs_cifti_tools
  2. This installation relies on a containerized simnibs version existing at /panfs/roc/groups/8/faird/shared/code/internal/pipelines/container_simnibs/sing_test_simnibs_alone_debian.sif plus the existing matlab installation version
    Note: For the FEM generation stage, when calling the container the following lines are explicitly written " module load matlab/R2019a" this line must be written before calling the container to allow the container access to the matlab installation version available on MSI "-B /panfs/roc/msisoft/matlab/R2019a/:/usr/local/bin/matlab/" this mounts matlab into a local folder within the container
  3. For an example on using the code for the Efield Generator, follow the instructions at Running an example