Anonymize & Upload EDFs to ieeg.org

What this page tells you

Anonymize Mxene EDFs on cnt1 with anonymize_edfs.sh (-n, -i, -d, -o required; date-shifts to 1/1/2000), create an ieeg-dataset.ini channel mapping, then upload the deid folder with ieeg upload-directory.

Mxene EEG Processing/Uploading

1. move EDF file into cnt-fs
   1. For Mxene EEG: /eeg_raw/Mxene_project/RIDXXXX/original
2. de-identify EDF file
   1. Open Mobaxterm, and in cnt1, navigate to /project/eeg_process/programs/edf_anonymize
   2. in the command line run bash anonymize_edfs.sh -n NAME -i ID -d DIRECTORY_INPUT -o DIRECTORY_OUTPUT -a ADD_DATE -s SUBTRACT_DATE
      1. This will create a new EDF file with anonymized headers
         1. the de-identified file will be named <original_filename>_deid.edf
      2. Options
         1. -n : Removes the patient name from the header and replaces with a new name specified here. I recommend inputting deid
         2. -i : Removes the patient ID from the header and replaces with a new ID specified here. I recommend inputting deid
         3. -d : The path to the source directory where the EDF is stored. E.g. /mnt/cnt-fs/eeg_raw/Mxene_project/RIDXXXX/original
         4. -o : The path to the output directory where the deid EDF will be stored. E.g. /mnt/cnt-fs/eeg_raw/Mxene_project/RIDXXXX/deid
         5. -a : The default behavior will date shift the recording date of the EDF to 1/1/2000. Instead, if you would like to date shift by adding days to the original recording date, input the number of days you would like to add
         6. -s : The default behavior will date shift the recording date of the EDF to 1/1/2000. Instead, if you would like to date shift by subtracting days from the original recording date, input the number of days you would like to subtract
      3. The -n , -i , -d and -o flags are mandatory. It will error if any of these are missing
      4. The -a and -s flags are optional. By default, without these parameters the code will date shift the EDF to 1/1/2000, and this is generally recommended. If both parameters are included accidentally, then the code will error.
3. create the ieeg-dataset.ini channel mapping file
   1. copy the ieeg-dataset.ini template file and paste into cnt-fs /eeg_raw/Mxene_project/RIDXXXX/deid
   2. open the ieeg-dataset.ini file through Notepad, and edit the channel mappings as needed for the EDF recording
      1. Template: channels=Fp1,Fp2,F7,F8,....
      2. Notes:
         1. Each channel is separated by a comma. Be sure that there are no spaces between each channel
         2. The order of the channels matter! This will determine the order of the channels in ieeg.org
         3. If you need to rename a channel, it will look like this: channels=FP1:Fp1,FP2:Fp2,F7,F8,T3:T7,T4:T8,....
            1. The old channel name is specified to the left of the colon, and the new channel name is specified to the right of the colon
         4. DO NOT rename the ieeg-dataset.ini file or else the upload process will error
4. upload the deid edf folder to ieeg.org
   1. make sure the <original_filename>_deid.edf file and the ieeg-dataset.ini channel mapping file are both in the cnt-fs /eeg_raw/Mxene_project/RIDXXXX/deid directory, and no other files are in there
   2. In cnt1, navigate to /project/eeg_process/programs/ieeg-cli-1.14.60
   3. run ./ieeg upload-directory -n 'Human_Data/Hospital of the University of Pennsylvania/Mxene/RIDXXXX' '/mnt/cnt-fs/eeg_raw/Mxene_project/RIDXXXX/deid'
   4. check ieeg.org and verify the EDF looks good