Exporting pre-processed raw data as EDF

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Hi, I used brainstorm to do the preprocessing (low and high band filter, notch, bad channels and ICA for heartbeat and blink). I exported the last ''raw'', the one with all the preprocessing. However, once the file opened, it seems the bad channels were not delete. I would like to know which steps of the preprocessing were exported and which steps I need to re-do. Can you specify that please?
Thank you

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Hi @mmbriand,the EDF is a simple format for biomedical signals, it does have some limitations in terms of what it can be stored in it. Let me expand on what is going on with your pre-processing:

In Brainstorm

  1. Frequency filters are applied on the "raw" data signals, creating a new file with the filtered signals. So if you export at this point the EDF file will have filtered signals
    https://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter

  2. Bad channels, are just a label in Brainstorm that indicates if the channels will be used for further analyses. The EDF definition does not have metadata on bad/good channels, thus marking channels as bad/good in Brainstorm does not have any impact on the exported signals to the EDF file
    https://neuroimage.usc.edu/brainstorm/Tutorials/BadChannels

  3. Some processing methods such as EEG re-referencing, SSP and ICA, are not applied on the data when computed, but rather they are stored as linear projectors. The EDF specification does not store linear operation on the signals. So, if you export the data with projectors, these will not be applied on the signals in the EDF file.
    https://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsSsp

Do not worry, there is hope on exporting data from Brainstorm to EDF keeping most of the pre-processing:

  1. Apply frequency filters as you have

  2. Mark bad/good channels

  3. Compute projectors (SSP/ICA/Re-referencing). Their computation will ignore the bad channels from Step 2.

  4. Now, apply those projectors, so they are not anymore a linear projector applied on the fly, but applied on the data. This is done with the process Artifacts > Apply SSP and CTF compensation. This will create a new raw folder with the | clean label
    You will notice, that if you open the option Artifacts > Select active projectors it is not possible to change them, they are already applied to the data.

  5. Finally, you can export this | clean raw file as EDF, it will have the frequency filters and projectors applied to the data. Unfortunately, the bad channels will remain visible in the EDF file, but remember, they were not considered on computing the projectors.

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Thank you very much for your answer. This is really helping