I am working on removing the blink artifact using the PCA in mne. We have a couple of subjects whose channels go flat for a few seconds(EEG, MEG, EOG and ECG) including the stimuli. I was wondering if there is a way to skip that part of the raw.fif file while using the mne_process_raw command to create an EOG projector.
I was wondering if this skip can be done when we create a projector just like how we can introduce a descriptor file when we are creating averages using mne_process_raw. I wanted to know of gradflat/magflat/eegflat parameters can be included in the mne_process_raw command. (I don't think this option is there in the mne_browse_raw gui structure.)
Do let me know if there is another way of omitting the blank data in the fif file when creating a projector.
There is no way to specify the "flat" limits on the command line of mne_process_raw, unfortunately.
However, in the Averaging preferences dialog (Adjust menu) of mne_browse_raw there are "no signal" limits (flat parameters) which affect the interactive computation of the projection operators.
Hi Candida,
Perhaps you could make SSPs in 2 steps:
(1) Make a cov file for your blinks using a cov descriptor where you can
specify flat channel limits
(2) Use mne_cov2proj
Hi Candida,
couple of years back, I wrote a function in Matlab that compute
projections from raw fif file on supplied event file and store them in mne
format. In Matlab we can custom the kind of data rejection you want.
Actually, MNE-Python may have projection calculations, too.
Yes, mne-python has scrips to compute SSP projectors for ECG and EOG.
Assuming you have mne-python set up*, run "mne_compute_proj_eog.py
--help" from the command line to see the available options. The script
will detect EOG events and then compute projectors. The script doesn't
have the option to discard flat sections, but if the EOG channels are
flat, there won't be any events.