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CHOP Stim Seizures EEG Processing

What this page tells you

Processing commands for CHOP stim seizure data: natus2mef with natus-converter-1.2.14 using paths under /mnt/cnt-fs/chop_fs/CHOP_stim_seizures, mefvalidate, redact annotations, copy annotations and montages, then upload to Human_Data/CHOP/CHOP_Stim_Seizures/CHOPXXX.

Open VDI

Natus to mef conversion

  • ssh cnt1
  • cd /project/eeg_process/programs/natus-converter-1.2.14
  • screen -S CHOPXXX_convert
  • ./natus2mef -c /mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data/CHOPXXX_natusDir.txt -m /mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data/CHOPXXX_channelMapping.txt -o ../../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef >/mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data/CHOPXXX_convert_log 2>&1
  • Check to make the convert log says "Processing successful" before moving to the next steps.

Mef validate

  • cd /project/eeg_process/programs/ieeg-cli-latest
    • ./mefvalidate ../../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef/*.mef | grep PASS
    • ./mefvalidate ../../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef/*.mef | grep FAIL

Redact the annotations

  • cd /project/eeg_process/programs/
  • python redact_annots_python3.py ../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef/annotations.iann.json ../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef/annotations_edit.iann.json

Once you redact the annotations (any with PHI), enter the mef file that you just created with:

  • cd /project/eeg_process/CHOPXXXspontaneous_seizure_data/CHOPXXX_mef

copy over both annotations files and the montages, and then delete the original annotations file from the mef

  • cp -r annotations.iann.json /mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data
  • cp -r annotations_edit.iann.json /mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data
  • cp -r montages.imtg.json /mnt/cnt-fs/chop_fs/CHOP_stim_seizures/CHOPXXXspontaneous_seizure_data

Delete original annotations file if it has PHI before uploading!! (unless you made no edits)
rm -r annotations.iann.json

Upload to ieeg.org

  • cd /project/eeg_process/programs/ieeg-cli-latest
  • screen -S CHOPXXX_ieeg_upload
  • ./ieeg upload-directory -n 'Human_Data/CHOP/CHOP_Stim_Seizures/CHOPXXX' '../../CHOPXXXspontaneous_seizure_data/CHOPXXX_mef'