Analysis AWS: Difference between revisions
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== Accessing compute resources on AWS: ==
Speak with Jeff Stout to get the current IP address and PEM key <br>
<br>
chmod 400 AWS.pem
${PATH} is the path to the PEM key provided to you
ssh -X -i
'''Windows Laptops''' do not have X11 installed natively. Download an Xterm software for visualization. <br>
MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html
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PyCTF website: https://megcore.nih.gov/index.php/MEG_Software_and_Analysis#MEG_Core_pyctf_tools_ported_to_Python_3 <br>
conda activate workshop # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed
ipython
import eelbrain, mne, pyctf
'''CTF software'''
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'''Afni'''
afni -dset $MRI_file
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Latest revision as of 12:15, 7 November 2019
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 user1@ec2-3-230-155-59.compute-1.amazonaws.com
Windows Laptops do not have X11 installed natively. Download an Xterm software for visualization.
MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html
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: https://hnn.brown.edu/
conda deactivate hnn
MNE python, Eelbrain, PyCTF
MNE website: https://mne.tools/stable/index.html
Eelbrain website: https://eelbrain.readthedocs.io/en/stable/
PyCTF website: https://megcore.nih.gov/index.php/MEG_Software_and_Analysis#MEG_Core_pyctf_tools_ported_to_Python_3
conda activate workshop # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed ipython import eelbrain, mne, pyctf
CTF software
singularity shell /opt/ctf/ctf.img $ctf_command
singularity exec /opt/ctf/ctf.img $ctf_command
SAM version 5
sam_cov ... sam_3d ...
Afni
afni -dset $MRI_file