Difference between revisions of "Analysis AWS"

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singularity exec /opt/ctf/ctf.img $ctf_command
 
singularity exec /opt/ctf/ctf.img $ctf_command
  +
  +
SAM version 5
  +
sam_cov ...
  +
sam_3d ...
   
 
Afni
 
Afni

Revision as of 19:09, 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 or Eelbrain

 conda activate workshop  (This environment has MNE and Eelbrain 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