Analysis AWS

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For Workshop members without access to computing resources - Preconfigured Amazon Web Services servers can be used

Accessing compute resources on AWS:

Speak with Jeff Stout to get the current IP address and PEM key
${PATH} is the path to the PEM key provided to you

 ssh -X -i ${PATH}/AWS.pem ubuntu@IP_ADDRESS_PROVIDED

Jupyter Notebook Over a Remote Connection

1) Run one terminal to start the notebook and forward the outputs to local web browser:

 ssh -i AWS.pem -L 8887:localhost:8887  ubuntu@IP_ADDRESS
 conda activate workshop  
 jupyter notebook --no-browser --port=8887

2) Copy the output of the jupyter notebook command (see example below) and enter into your laptop web browser (Firefox, Chrome, etc.). Do not click on the link - it will try to launch on the AWS computer


3) Use the jupyter notebook to analyze MEG data with python tools


Installed software

Human Neocortical Neurosolver

 #hnn is installed in the system level python >> may need to conda deactivate first

MNE python, Eelbrain, PyCTF

 conda activate workshop  (This environment has MNE, Eelbrain, and PyCtf installed)

CTF software

 singularity shell /opt/ctf/ctf.img
 singularity exec /opt/ctf/ctf.img $ctf_command

SAM version 5

 sam_cov ...
 sam_3d ...


 afni -dset $MRI_file


SAM v5 singularity ? >> CTF Afni Jupyter HNN


Freesurfer Reinstall MNE python Pyctf FSL Brainstorm Fieldtrip Spyder