Post template

Author

RPM

Published

March 29, 2023

A better way is to copy all the files from the “psy4911/share” folder to your HiPerGator (HPG) folder. The rsync command for moving files between directories on HPG is described here. Copying_files_between_directories with rsync You will want to go to the shared folder on HPG first and open a terminal (see button outlined green in the schreenshot below). ephys folders to copy from shared folder to your own folder

Then if you copy and paste these commands into terminal it will do the work for you: rsync -av /blue/psy4911/share/ket_ephys/ket_annot /blue/psy4911/yourusername/ket_ephys/ rsync -av /blue/psy4911/share/ket_ephys/ket_annot_segs /blue/psy4911/yourusername/ket_ephys/ rsync -av /blue/psy4911/share/ket_ephys/hi-ket /blue/psy4911/yourusername/ket_ephys/

For the files in the hi-ket folder there’s another script (and a package named NEO ) that’s required to convert them from .plx files to .fif files.

Required python packages: - NEO - NEO repo - NEO documentation - MNE - MNE Tutorial: importing data from NEO

Code for the file conversion:

The main thing is that it takes 15 minutes per file on hipergator (HPG) when it’s set up like a laptop computer. When you configure HPG to run your jupter notebook in high-performance mode, it takes only a minute or two per file. So, what would take 5 hours for 20 files, ends up taking only a half hour.

An even bigger savings comes when doing machine learning / AI with deeplabcut on HPG.