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ncsl / seek

(Stereotatic ElectroEncephalography Kit) Run reconstruction, co-registration, electrode localization and surface/atlas rendering for iEEG, T1 MRI and CT data.

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Docker and/or Singularity Container for Pipelines

adam2392 opened this issue · comments

commented

Describe the problem

Currently the pipelines to run require usage of various 3rd party softwares that might not be trivial to setup and install, such as FreeSurfer, FSL, Gawk, Blender, MRTrix3, etc.

Describe your solution

A docker container running the installation, so we can run all pipelines thru the container.

Describe possible alternatives

I think Docker is the best way to do this.

commented

A modularized docker container, could look like just a high-level docker container that pulls in images and adds the following commands:

  1. FreeSurfer: https://hub.docker.com/r/freesurfer/freesurfer/
  2. FSL: https://hub.docker.com/r/vistalab/fsl-v5.0/dockerfile
  3. Blender: https://github.com/ikester/blender-docker
  4. Add sudo apt-get install -y gawk
  5. SPM12: https://github.com/spm/spm-docker/blob/master/octave/Dockerfile
  6. Octave: https://wiki.octave.org/Octave_for_GNU/Linux

This way, we can axe certain dependencies when needed.

commented
  • All of the above
  • Silent install of matlab (only requiring user's file installation key from Mathworks)
  • Setting env. variables

Tested on:

  • Linux (Ubuntu 18.04)
  • Windows (WSL2)
  • Mac