Analysis AWS: Difference between revisions
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== Accessing compute resources on AWS: == |
== Accessing compute resources on AWS: == |
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Speak with Jeff Stout to get the current IP address and PEM key <br> |
Speak with Jeff Stout to get the current IP address and PEM key <br> |
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<br> |
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chmod 400 AWS.pem |
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${PATH} is the path to the PEM key provided to you |
${PATH} is the path to the PEM key provided to you |
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ssh -X -i |
ssh -X -i AWS.pem user1@ec2-3-230-155-59.compute-1.amazonaws.com |
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'''Windows Laptops''' do not have X11 installed natively. Download an Xterm software for visualization. <br> |
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MobaXterm has been tested to work: https://mobaxterm.mobatek.net/download.html |
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== Jupyter Notebook Over a Remote Connection == |
== Jupyter Notebook Over a Remote Connection == |
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== Installed software == |
== Installed software == |
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Human Neocortical Neurosolver |
'''Human Neocortical Neurosolver ''' <br> |
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HNN website: https://hnn.brown.edu/ |
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conda deactivate |
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hnn |
hnn |
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#hnn is installed in the system level python >> may need to conda deactivate first |
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MNE python, Eelbrain, PyCTF |
'''MNE python, Eelbrain, PyCTF''' <br> |
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MNE website: https://mne.tools/stable/index.html <br> |
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Eelbrain website: https://eelbrain.readthedocs.io/en/stable/ <br> |
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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> |
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ipython |
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import eelbrain, mne, pyctf |
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CTF software |
'''CTF software''' |
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singularity shell /opt/ctf/ctf.img |
singularity shell /opt/ctf/ctf.img |
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$ctf_command |
$ctf_command |
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singularity exec /opt/ctf/ctf.img $ctf_command |
singularity exec /opt/ctf/ctf.img $ctf_command |
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SAM version 5 |
'''SAM version 5''' |
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sam_cov ... |
sam_cov ... |
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sam_3d ... |
sam_3d ... |
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Afni |
'''Afni''' |
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afni -dset $MRI_file |
afni -dset $MRI_file |
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==Done== |
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SAM v5 |
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singularity ? >> CTF |
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Afni |
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Jupyter |
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HNN |
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==TODO== |
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Freesurfer |
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Reinstall MNE python |
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Pyctf |
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FSL |
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Brainstorm |
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Fieldtrip |
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Spyder |
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Latest revision as of 11:15, 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