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

 chmod 400 AWS.pem

${PATH} is the path to the PEM key provided to you

 ssh -X -i AWS.pem

Windows Laptops do not have X11 installed natively. Download an Xterm software for visualization.
MobaXterm has been tested to work:

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 website:

 conda deactivate

MNE python, Eelbrain, PyCTF
MNE website:
Eelbrain website:
PyCTF website:

 conda activate workshop  # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed
 import eelbrain, mne, pyctf

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