Beauchamp:DownloadDataPenn

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Brain picture
Beauchamp Lab




Download iEEG data from ieeg.org (UPENN data)

Once you've received confirmation (usually from Dhanya/Ashley) that data are available on the ieeg.org portal, you can download data with the DownloadFromiEEGorg.m script. The script is located on the server in the rave_data directory. You need to connect to beauchamplab server to use this script. Here are the steps:

Connect to MacPro

Connect to the server, in Terminal, type in:

 ssh beauchamplab@beauchampsrv.bdc.bcm.edu

When asked "Are you sure you want to continue?", Answer "yes" When asked for the password, type in the beauchamplab password. If you see prompt: `(base) beauchamplab@beauchampsrv ~ % ` you are on the server now

If you get the error:

 ssh: Could not resolve hostname beauchampsrv.bdc.bcm.edu: nodename nor servname provided, or not known

You need to (re)connect to the BCM VPN or try accessing the server from the campus network (cf. https://vpn.bcm.edu/).

Running the script

Navigate to script location and start headless matlab

 cd /Volumes/PennRAID/Dropbox (PENN Neurotrauma)/BeauchampServe/rave_data
 /Applications/MATLAB_R2020a.app/bin/matlab -nodesktop -nosplash

Start the downloading script in matlab in terminal, specifying the ProjectID and the runs (you must use double quotes " not ' when concatenating run names, else matlab creates a length 1 character array)

 DownloadFromiEEGorg ("HUP217_Cohort2", ["run1","run2","run3","run4","run5"])

The script attempts to download only non-zero data by querying the event annotations. If there are more than 2 events, the user will be asked which events are correct, e.g.:

 Found multiple events!
 (1) Mask run 1
 (2) Tech notation: Video/EEG monitoring taking place
 (3) mask task run 1 end
 Pick two events to use for data range(separated by comma): 1, 3

Before downloading the data, the user confirms the size of the data:

 About to download 434.926758 seconds of data at 1024 Hz from 154 channels.
 Download the data? [Y]/n?

Raw data will be automatically downloaded to the rave_raw directory, organized by subject and run name (/Volumes/OneDrive/data/rave_data/raw/HUP211/run#). Confirmation of data download and photodiode detection are provided, followed by writing out the channel labels and detected sample rate to files in the subject's top-level directory.

 Writing out data to disk...done.
 Looking for photodiode on DC1...found. Downloading...done.
  Saving to photodiode.pd in /Volumes/OneDrive/data/rave_data/raw/HUP212/run1
 Writing out channel labels subject raw dir...done.
 Sample rate is: 1024. Writing to subject folder...done.

Note: If you requested more than one run, the script will effectively run once per run.

For the AV_NoisyWords project, the naming is different (adding cohort):

 DownloadFromiEEGorg ("HUP217_Cohort2", ["run1","run2","run3","run4","run5"])

Repeat the other steps to confirm downloading. You have to answer the following 'Y' before each run to be downloaded:

   About to download ####### seconds of data at 1024 Hz from ### channels.
   Download the data? [Y]/n?

Optional script parameters

You can change the ieeg.org user name, password file, and save location by specifying optional parameters:

 DownloadFromiEEGorg (subject, block, path_for_data, ieeg_user_name, path_to_pwd_file) 

For example, if you want to save the raw data to the desktop:

 DownloadFromiEEGorg ("HUP211", ["run1","run2"],"/Users/beauchamplab/Desktop")

Finishing up

To exit matlab, use the quit function

 >> quit()
 (base) beauchamplab@beauchampsrv rave_data % 

To terminate the ssh connection:

 ctrl+d
 Connection to beauchampsrv.bdc.bcm.edu closed.