Difference between revisions of "Analysis AWS"

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# Under Construction
 
   
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''' For Workshop members without access to computing resources - Preconfigured Amazon Web Services servers can be used'''
   
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== Accessing compute resources on AWS: ==
# Server Config
 
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Speak with Jeff Stout to get the current IP address and PEM key <br>
## google > fedora aws > select the AMI number for N.Virginia
 
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<br>
## In AWS > launch instance > search for AMI number > (Under community) > Launch
 
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chmod 400 AWS.pem
### https://alt.fedoraproject.org/cloud/
 
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${PATH} is the path to the PEM key provided to you
#Determine an image (search for fedora in community)
 
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ssh -X -i AWS.pem user1@ec2-3-230-155-59.compute-1.amazonaws.com
#Create a keypair and download the key
 
##The download will be in the form of a .pem file
 
## We will need to distribute this key to the users
 
#Launch the instance
 
#Log into the instance using ssh
 
   
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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 ==
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1) Run one terminal to start the notebook and forward the outputs to local web browser:
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ssh -i AWS.pem -L 8887:localhost:8887 ubuntu@IP_ADDRESS
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conda activate workshop
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jupyter notebook --no-browser --port=8887
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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
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[[file:JupyterAws2.png]]
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3) Use the jupyter notebook to analyze MEG data with python tools
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[[File:TestJupyter.png]]
   
# Freesurfer
 
# MNE python
 
# pyctf
 
# SAM v5
 
# Afni
 
# singularity ? >> CTF (need to use workstation version of fedora)
 
# Eelbrain (conda forge)
 
# Jupyter
 
# Forward sim HNN software
 
# FSL
 
 
<br>
 
<br>
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'''Matlab Based'''
 
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== Installed software ==
# Brainstorm
 
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'''Human Neocortical Neurosolver ''' <br>
# Fieldtrip
 
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HNN website: https://hnn.brown.edu/
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conda deactivate
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hnn
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'''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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conda activate workshop # This conda environment has the MNE, Eelbrain, and PyCtf toolboxes installed
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ipython
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import eelbrain, mne, pyctf
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'''CTF software'''
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singularity shell /opt/ctf/ctf.img
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$ctf_command
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singularity exec /opt/ctf/ctf.img $ctf_command
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'''SAM version 5'''
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sam_cov ...
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sam_3d ...
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'''Afni'''
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afni -dset $MRI_file

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

 JupyterAws2.png

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

 TestJupyter.png


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