Difference between revisions of "Analysis AWS"

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


MNE python or Eelbrain
MNE python, Eelbrain, PyCTF
conda activate workshop (This environment has MNE and Eelbrain installed)
conda activate workshop (This environment has MNE, Eelbrain, and PyCtf installed)


CTF software
CTF software

Revision as of 19:10, 31 October 2019

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

To access the compute system:

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

Installed software
Human Neocortical Neurosolver

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

MNE python, Eelbrain, PyCTF

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

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



  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