Analysis AWS

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