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Mxene EEG Processing & Upload

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What this page tells you

Export the Mxene and clinical recordings from Natus (EEG database) as EDF into cnt-fs/eeg_raw/Mxene_project/RIDXXXX subfolders, copy the .ini channel mapping from a previous patient, run anonymize_edfs.sh in cnt1 to create _deid.edf files, move originals to Original_edfs, then ieeg upload-directory each folder to the Mxene_Electrode project.

Exporting the data:

  • The data will be exported into cnt-fs
  • In cnt-fs, create a folder titled RIDXXXX in cnt-fs/eeg_raw/Mxene_project

  • Inside this folder (cnt-fs/eeg_raw/Mxene_project), create 2 folders called RIDXXXX_Mxene and RIDXXXX_Clinical
    cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Mxene
    cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Clinical

  • Create a data collection file and document the actual times and dates that the Mxene and Clinical recordings were done. You can leave this file in the RIDXXXX folder.

    • This is just for record-keeping to make sure we have the actual dates/times documented somewhere. We do not need this for processing. Look at a previous patient for an example.
  • Log into the remote desktop to access the Natus computer
  • In the Natus computer, go to Database on the upper left hand side, and make sure to select EEG instead of EMU
  • Scroll to the date that the test was completed
  • Right click on the clip you want to export -> select export -> choose edf file -> video should be unchecked, but uncheck if not -> choose folder you need (RIDXXX_Mxene)
  • Export the data as an edf file!
  • Export both the research file that you did AND the clinical eeg recorded. These will be 2 separate files
  • Export the Mxene file in the following folder in cnt-fs: eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Mxene
  • Export the Clinical file in the following folder in cnt-fs: eeg_raw/Mxene_project/RIDXXX/RIDXXXX_Clinical

Anonymizing edf files:

  • We are first going to anonymize the edf files and then upload them to ieeg
  • Enter the VDI and mount cnt-fs: Mounting cnt-fs (Mounting cnt-fs)
  • Copy over the Mxene .ini file (channel mapping file) from the previous patient's RIDXXXX_Mxene folder into the current patient’s RIDXXXX_Mxene folder
    • It is the same channel mapping file because the same channels are used!
  • Copy over the Clinical .ini file (channel mapping file) from the previous patient's RIDXXXX_Clinical folder into the current patient’s RIDXXXX_Clinical folder
    • It is the same channel mapping file because the same channels are used!
  • At this point, you should have 2 completed folders for the current patient in cnt-fs/eeg_raw/Mxene_project/RIDXXXX: 1st folder (RIDXXXX_Mxene) with the Mxene edf file + Mxene .ini file and then the 2nd folder (RIDXXX_Clinical) with the Clinical edf file + Clinical .ini file
  • Now open Mobaxterm
  • Enter cnt1 with the following code:
    • ssh cnt1

  • move EDF file into cnt-fs

    1. For Mxene EEG: cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXX_Mxene

  • de-identify EDF file

    1. Open Mobaxterm, and in cnt1, navigate to
      cd 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:
        _deid.edf
      1. 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
        ex: cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Mxene
        1. -o : The path to the output directory where the deid EDF will be stored. E.g. cnt-fs/eeg_raw/Mxene_project/RIDXXXX/deid
          2. -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
          3. -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
      1. The -n , -i , -d and -o flags are mandatory. It will error if any of these are missing
      2. 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

  • Now at this point, the script will have created 2 anonymized edf files with .deid at the end!

    • These are the ones we are going to upload to ieeg instead of the original edf files!
  • Go into the file explorer and enter cnt-fs
  • Enter eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Mxene
  • Move the original edf file out of this folder into the folder titled "Original_edfs" in cnt-fs/eeg_raw/Mxene_project
  • Do the same for the original edf file in eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Clinical

  • All that should be left in the Mxene and Clinical folders for the current patient are the anonymized .deid edf files and the respective .ini files

  • 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

Upload anonymized edf files to ieeg:

  • Go back to cnt1 in Mobaxterm
  • Enter the ieeg upload directory with this code:
    • cd /project/eeg_process/programs/ieeg-cli-latest
  • First upload the Mxene edf with this code:
    • ./ieeg upload-directory -n 'Human_Data/Hospital of the University of Pennsylvania/Mxene_Electrode/RIDXXXX_Mxene' '/mnt/cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Mxene'
  • Then upload the Clinical edf with this code:
    • ./ieeg upload-directory -n 'Human_Data/Hospital of the University of Pennsylvania/Mxene_Electrode/RIDXXXX_Clinical' '/mnt/cnt-fs/eeg_raw/Mxene_project/RIDXXXX/RIDXXXX_Clinical'

You are all done!! 🙂