Difference between revisions of "Analysis AWS"

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''' For Workshop members without access to computing resources - Amazon Web Services servers can be used'''
# Under Construction
 
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To access the system:
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ssh -X -i ~/Downloads/AWS.pem ubuntu@IP_ADDRESS_PROVIDED
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Human Neocortical Neurosolver
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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 or Eelbrain
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conda activate workshop (This environment has MNE and Eelbrain installed)
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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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--OR--
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singularity exec /opt/ctf/ctf.img $ctf_command
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Afni
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afni -dset $MRI_file
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Revision as of 19:05, 31 October 2019

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

To access the system:

 ssh -X -i ~/Downloads/AWS.pem ubuntu@IP_ADDRESS_PROVIDED

Human Neocortical Neurosolver

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

MNE python or Eelbrain

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

CTF software

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

Afni

 afni -dset $MRI_file



  1. Server Config
    1. google > fedora aws > select the AMI number for N.Virginia
    2. In AWS > launch instance > search for AMI number > (Under community) > Launch
      1. https://alt.fedoraproject.org/cloud/
  2. Determine an image (search for fedora in community)
  3. Create a keypair and download the key
    1. The download will be in the form of a .pem file
    2. We will need to distribute this key to the users
  4. Launch the instance
  5. Log into the instance using ssh


Conda installed Conda deactivate >> hnn Conda activate nih >> mne or eelbrain.....


  1. Freesurfer
  2. MNE python
  3. pyctf

Done # SAM v5

  1. Afni ###INSTALL ME neurodebian
  2. singularity ? >> CTF (need to use workstation version of fedora) << may need to compile for ubuntu or use 2.6
  3. Eelbrain (conda forge)
  4. Jupyter

Done# Forward sim HNN software

  1. FSL ###Install outside of neurodebian
  2. Brainstorm (compiled)


Matlab Based

  1. Brainstorm
  2. Fieldtrip